Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008094.1 Hibiscus syriacus cultivar Beakdansim tig00110610_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 9952466
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 29 of 43
Found at i:6124614 original size:18 final size:19
Alignment explanation
Indices: 6124568--6124612 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
6124558 AAGTTCTCTC
*
6124568 TTTTC-TTTTCTTTTCAAG
1 TTTTCATTTTATTTTCAAG
6124586 TTTTCATTTTATTTT-AAG
1 TTTTCATTTTATTTTCAAG
6124604 TTTT-ATTTT
1 TTTTCATTTT
6124613 TAAACATGCT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
17 5 0.20
18 12 0.48
19 8 0.32
ACGTcount: A:0.16, C:0.09, G:0.04, T:0.71
Consensus pattern (19 bp):
TTTTCATTTTATTTTCAAG
Found at i:6128512 original size:37 final size:36
Alignment explanation
Indices: 6128437--6128512 Score: 100
Period size: 36 Copynumber: 2.1 Consensus size: 36
6128427 TTTTTATATT
*
6128437 TTTAATTTTGTAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
* *
6128473 TTTAATTTTTTAAAGAAAA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAA-AAAATTATATAAATATTAT-CAA
6128510 TTT
1 TTT
6128513 GTAATATTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
36 26 0.74
37 9 0.26
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.47
Consensus pattern (36 bp):
TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
Found at i:6140697 original size:29 final size:31
Alignment explanation
Indices: 6140631--6140697 Score: 75
Period size: 29 Copynumber: 2.2 Consensus size: 31
6140621 TTAAAATGGC
** *
6140631 CATTTTGGTCCCTAAACTTTTCCAAAGTTTA
1 CATTTTGGTAACTAAACTTTTCCAAAATTTA
* *
6140662 TACTTTGGTAACTAAAC-TTT-CAAAATTTA
1 CATTTTGGTAACTAAACTTTTCCAAAATTTA
6140691 CATTTTG
1 CATTTTG
6140698 TCATTTACCA
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
29 13 0.45
30 3 0.10
31 13 0.45
ACGTcount: A:0.30, C:0.18, G:0.09, T:0.43
Consensus pattern (31 bp):
CATTTTGGTAACTAAACTTTTCCAAAATTTA
Found at i:6143301 original size:17 final size:17
Alignment explanation
Indices: 6143275--6143312 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
6143265 TTAATATTTT
*
6143275 GTATTTAATTTATTTAA
1 GTATTAAATTTATTTAA
6143292 GTATTAAATTTATTTAA
1 GTATTAAATTTATTTAA
6143309 -TATT
1 GTATT
6143313 TTACTTATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 4 0.20
17 16 0.80
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (17 bp):
GTATTAAATTTATTTAA
Found at i:6146126 original size:37 final size:38
Alignment explanation
Indices: 6146057--6146128 Score: 128
Period size: 38 Copynumber: 1.9 Consensus size: 38
6146047 ACCCGAACCT
6146057 GACCCGAATATCACACTTAAAAAAACCCGACCCGACTC
1 GACCCGAATATCACACTTAAAAAAACCCGACCCGACTC
*
6146095 GACCCGAATATCACACTT-AAAAATCCCGACCCGA
1 GACCCGAATATCACACTTAAAAAAACCCGACCCGA
6146129 ACAAAATAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
37 15 0.45
38 18 0.55
ACGTcount: A:0.39, C:0.36, G:0.11, T:0.14
Consensus pattern (38 bp):
GACCCGAATATCACACTTAAAAAAACCCGACCCGACTC
Found at i:6146699 original size:14 final size:14
Alignment explanation
Indices: 6146680--6146714 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
6146670 AAAATAAATT
*
6146680 ATATTTTTTGAAAA
1 ATATTTTCTGAAAA
6146694 ATATTTTCTGAAAA
1 ATATTTTCTGAAAA
*
6146708 ATGTTTT
1 ATATTTT
6146715 ATGATGTTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.37, C:0.03, G:0.09, T:0.51
Consensus pattern (14 bp):
ATATTTTCTGAAAA
Found at i:6146884 original size:20 final size:20
Alignment explanation
Indices: 6146832--6146885 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 20
6146822 AACTTAATAT
6146832 TATTATTTTTAAAATATTAAAA
1 TATTATTTTT--AATATTAAAA
* *
6146854 TAATT-TATTTATTATTAAAA
1 T-ATTATTTTTAATATTAAAA
6146874 TATTATTTTTAA
1 TATTATTTTTAA
6146886 AATTTCATTA
Statistics
Matches: 26, Mismatches: 4, Indels: 6
0.72 0.11 0.17
Matches are distributed among these distances:
19 3 0.12
20 15 0.58
22 5 0.19
23 3 0.12
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
TATTATTTTTAATATTAAAA
Found at i:6146885 original size:14 final size:14
Alignment explanation
Indices: 6146862--6146931 Score: 54
Period size: 14 Copynumber: 5.0 Consensus size: 14
6146852 AATAATTTAT
6146862 TTATTATTAAAATA
1 TTATTATTAAAATA
*
6146876 TTATTTTTAAAAT-
1 TTATTATTAAAATA
*
6146889 TTCATTAATAAAAATA
1 TT-ATT-ATTAAAATA
* **
6146905 TTAATATTAGTATA
1 TTATTATTAAAATA
*
6146919 TT-TTATTGAAATA
1 TTATTATTAAAATA
6146932 AAAATATTAT
Statistics
Matches: 42, Mismatches: 11, Indels: 7
0.70 0.18 0.12
Matches are distributed among these distances:
13 9 0.21
14 23 0.55
15 8 0.19
16 2 0.05
ACGTcount: A:0.46, C:0.01, G:0.03, T:0.50
Consensus pattern (14 bp):
TTATTATTAAAATA
Found at i:6146958 original size:33 final size:33
Alignment explanation
Indices: 6146895--6146958 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
6146885 AAATTTCATT
* **
6146895 AATAAAAATATTAATATTAGTATATTTTATTGA
1 AATAAAAATATTAAAATTAGTATAAATTATTGA
6146928 AATAAAAATATTATAAATTA-TATAAATTATT
1 AATAAAAATATTA-AAATTAGTATAAATTATT
6146959 TATTAAAGTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
33 22 0.81
34 5 0.19
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (33 bp):
AATAAAAATATTAAAATTAGTATAAATTATTGA
Found at i:6147051 original size:34 final size:34
Alignment explanation
Indices: 6146975--6147052 Score: 85
Period size: 33 Copynumber: 2.4 Consensus size: 34
6146965 AGTAATAGTG
6146975 TTATATT-ATATTTTAAAAATAGTAATTAGTATA
1 TTATATTAATATTTTAAAAATAGTAATTAGTATA
* *
6147008 TT-T-TAAATATCTTTATAAAATA-TTATTAGT-TA
1 TTATATTAATAT-TTTA-AAAATAGTAATTAGTATA
6147040 TTATATTAATATT
1 TTATATTAATATT
6147053 AAATATATAA
Statistics
Matches: 37, Mismatches: 3, Indels: 10
0.74 0.06 0.20
Matches are distributed among these distances:
31 1 0.03
32 9 0.24
33 15 0.41
34 12 0.32
ACGTcount: A:0.42, C:0.01, G:0.04, T:0.53
Consensus pattern (34 bp):
TTATATTAATATTTTAAAAATAGTAATTAGTATA
Found at i:6147217 original size:23 final size:23
Alignment explanation
Indices: 6147169--6147227 Score: 57
Period size: 23 Copynumber: 2.5 Consensus size: 23
6147159 AAATAATATC
* **
6147169 TTATATTATTATAATATAATTGA
1 TTATTTTATTATAATATAATAAA
6147192 TTATTTTATTATAATATTAA-AAA
1 TTATTTTATTATAATA-TAATAAA
*
6147215 TTATATTAATTAT
1 TTAT-TTTATTAT
6147228 TAGAAATATT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
23 20 0.67
24 10 0.33
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (23 bp):
TTATTTTATTATAATATAATAAA
Found at i:6148016 original size:12 final size:12
Alignment explanation
Indices: 6148001--6148065 Score: 51
Period size: 12 Copynumber: 5.1 Consensus size: 12
6147991 AGGTATATTT
*
6148001 TATTATATTTAA
1 TATTTTATTTAA
*
6148013 TATTTTA-TTAG
1 TATTTTATTTAA
6148024 TATTTTATTTAA
1 TATTTTATTTAA
*
6148036 CTATTTAAATTTTTTAA
1 -TA-TT---TTATTTAA
6148053 TATTTTATTTAA
1 TATTTTATTTAA
6148065 T
1 T
6148066 TAACTTTTTT
Statistics
Matches: 42, Mismatches: 5, Indels: 12
0.71 0.08 0.20
Matches are distributed among these distances:
11 10 0.24
12 17 0.40
13 2 0.05
14 2 0.05
15 2 0.05
16 2 0.05
17 7 0.17
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.63
Consensus pattern (12 bp):
TATTTTATTTAA
Found at i:6148017 original size:17 final size:18
Alignment explanation
Indices: 6147995--6148028 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
6147985 TCTTTAAGGT
6147995 ATATTTTATTA-TATTTA
1 ATATTTTATTAGTATTTA
6148012 ATATTTTATTAGTATTT
1 ATATTTTATTAGTATTT
6148029 TATTTAACTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (18 bp):
ATATTTTATTAGTATTTA
Found at i:6148060 original size:29 final size:30
Alignment explanation
Indices: 6147995--6148065 Score: 96
Period size: 29 Copynumber: 2.5 Consensus size: 30
6147985 TCTTTAAGGT
6147995 ATATTTTA-TT-ATATTTAATATTTTATTA
1 ATATTTTATTTAATATTTAATATTTTATTA
*
6148023 GTATTTTATTTAACTATTTAA-ATTTT-TTA
1 ATATTTTATTTAA-TATTTAATATTTTATTA
6148052 ATATTTTATTTAAT
1 ATATTTTATTTAAT
6148066 TAACTTTTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
28 8 0.21
29 17 0.45
30 6 0.16
31 7 0.18
ACGTcount: A:0.34, C:0.01, G:0.01, T:0.63
Consensus pattern (30 bp):
ATATTTTATTTAATATTTAATATTTTATTA
Found at i:6149765 original size:27 final size:27
Alignment explanation
Indices: 6149735--6149795 Score: 77
Period size: 27 Copynumber: 2.3 Consensus size: 27
6149725 AGCCATATTT
* *
6149735 GATGTCGCTACCCCCTTTCTCTTACCA
1 GATGTCGCCACCCCCTTTCACTTACCA
* * *
6149762 GATGCCTCCACCGCCTTTCACTTACCA
1 GATGTCGCCACCCCCTTTCACTTACCA
6149789 GATGTCG
1 GATGTCG
6149796 TCGCTGCTAC
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.16, C:0.39, G:0.15, T:0.30
Consensus pattern (27 bp):
GATGTCGCCACCCCCTTTCACTTACCA
Found at i:6150603 original size:22 final size:22
Alignment explanation
Indices: 6150575--6150621 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
6150565 ACAATAAAAT
6150575 TTTTACACATAAACGTAAATAA
1 TTTTACACATAAACGTAAATAA
6150597 TTTTACACATAAACGTAAATAA
1 TTTTACACATAAACGTAAATAA
6150619 TTT
1 TTT
6150622 AAATAATTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.47, C:0.13, G:0.04, T:0.36
Consensus pattern (22 bp):
TTTTACACATAAACGTAAATAA
Found at i:6151915 original size:50 final size:50
Alignment explanation
Indices: 6151856--6151981 Score: 155
Period size: 50 Copynumber: 2.5 Consensus size: 50
6151846 TTAGCAGGAA
* * * * *
6151856 AGCGCGCCCCCTGAACCGCGCTATATGTTGATTTGGCTCCACATGGATAT
1 AGCGCGCCCCCTGATCCGCGCTATACGGTGATCTGGCGCCACATGGATAT
* * *
6151906 AGCGCGCCCCCTG-TCCTGCGATATACGGTGATCTGGCGCCACGTGGGTAT
1 AGCGCGCCCCCTGATCC-GCGCTATACGGTGATCTGGCGCCACATGGATAT
*
6151956 AGTGCGCCCCCTGATCCGCGCTATAC
1 AGCGCGCCCCCTGATCCGCGCTATAC
6151982 CTGGATATCT
Statistics
Matches: 64, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
49 2 0.03
50 59 0.92
51 3 0.05
ACGTcount: A:0.17, C:0.33, G:0.27, T:0.23
Consensus pattern (50 bp):
AGCGCGCCCCCTGATCCGCGCTATACGGTGATCTGGCGCCACATGGATAT
Found at i:6152459 original size:111 final size:111
Alignment explanation
Indices: 6152265--6152486 Score: 390
Period size: 111 Copynumber: 2.0 Consensus size: 111
6152255 TGGAAATCAT
* *
6152265 ATATCTCTACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTACTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
** *
6152330 TATTTAGTTGATTGATTTAATGCATGATTATTAGATTAAGAATTAA
66 TAACTAGTTGATTCATTTAATGCATGATTATTAGATTAAGAATTAA
*
6152376 ATATCTCGACACTTTACTGATACGTTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTACTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
6152441 TAACTAGTTGATTCATTTAATGCATGATTATTAGATTAAGAATTAA
66 TAACTAGTTGATTCATTTAATGCATGATTATTAGATTAAGAATTAA
6152487 TTTTTGTAAT
Statistics
Matches: 105, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
111 105 1.00
ACGTcount: A:0.36, C:0.09, G:0.11, T:0.44
Consensus pattern (111 bp):
ATATCTCGACACTTTACTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
TAACTAGTTGATTCATTTAATGCATGATTATTAGATTAAGAATTAA
Found at i:6154055 original size:21 final size:21
Alignment explanation
Indices: 6154031--6154072 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
6154021 ATATGATGCA
*
6154031 GCCATCGCCACAGATGACCCC
1 GCCACCGCCACAGATGACCCC
*
6154052 GCCACCGTCACAGATGACCCC
1 GCCACCGCCACAGATGACCCC
6154073 TCCTGGAGGC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.24, C:0.48, G:0.19, T:0.10
Consensus pattern (21 bp):
GCCACCGCCACAGATGACCCC
Found at i:6161170 original size:10 final size:9
Alignment explanation
Indices: 6161150--6161180 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
6161140 TGAAAGTAAT
6161150 AAAAT-AAA
1 AAAATAAAA
6161158 AAAATAAAA
1 AAAATAAAA
6161167 AAAATAAAA
1 AAAATAAAA
6161176 AAAAT
1 AAAAT
6161181 GATGAGAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 5 0.23
9 17 0.77
ACGTcount: A:0.87, C:0.00, G:0.00, T:0.13
Consensus pattern (9 bp):
AAAATAAAA
Found at i:6161199 original size:9 final size:9
Alignment explanation
Indices: 6161147--6161206 Score: 52
Period size: 9 Copynumber: 6.7 Consensus size: 9
6161137 TAATGAAAGT
6161147 AATAAAATA
1 AATAAAATA
6161156 AA-AAAATA
1 AATAAAATA
*
6161164 AAAAAAATA
1 AATAAAATA
*
6161173 AAAAAAATGA
1 AATAAAAT-A
* *
6161183 TGAGAAAATA
1 -AATAAAATA
6161193 AATAAAAT-
1 AATAAAATA
6161201 AATAAA
1 AATAAA
6161207 GTATAAGAAT
Statistics
Matches: 44, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
8 14 0.32
9 22 0.50
10 2 0.05
11 6 0.14
ACGTcount: A:0.78, C:0.00, G:0.05, T:0.17
Consensus pattern (9 bp):
AATAAAATA
Found at i:6162440 original size:17 final size:16
Alignment explanation
Indices: 6162399--6162470 Score: 81
Period size: 17 Copynumber: 4.2 Consensus size: 16
6162389 ATTCATGCAT
6162399 CTAGTTCATTGAATAAA
1 CTAGTTCATT-AATAAA
*
6162416 GTTAGTTCATTAATTAAA
1 -CTAGTTCATTAA-TAAA
*
6162434 CTAGTTCATTCATCAAA
1 CTAGTTCATTAAT-AAA
6162451 CTAGTTCATTTAATAAA
1 CTAGTTCA-TTAATAAA
6162468 CTA
1 CTA
6162471 ACTCTTAATT
Statistics
Matches: 47, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
16 1 0.02
17 29 0.62
18 17 0.36
ACGTcount: A:0.39, C:0.14, G:0.08, T:0.39
Consensus pattern (16 bp):
CTAGTTCATTAATAAA
Found at i:6162892 original size:25 final size:25
Alignment explanation
Indices: 6162863--6162933 Score: 133
Period size: 25 Copynumber: 2.8 Consensus size: 25
6162853 ACCTAATTCA
6162863 AATCATCCAAACCAAGGGCTGATTT
1 AATCATCCAAACCAAGGGCTGATTT
6162888 AATCATCCAAACCAAGGGCTGATTT
1 AATCATCCAAACCAAGGGCTGATTT
*
6162913 AATCATTCAAACCAAGGGCTG
1 AATCATCCAAACCAAGGGCTG
6162934 TTCATATTCT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
25 45 1.00
ACGTcount: A:0.37, C:0.24, G:0.17, T:0.23
Consensus pattern (25 bp):
AATCATCCAAACCAAGGGCTGATTT
Found at i:6164933 original size:19 final size:19
Alignment explanation
Indices: 6164904--6164960 Score: 64
Period size: 21 Copynumber: 2.9 Consensus size: 19
6164894 AAAAAGAAGA
*
6164904 AGAAATGAGAGTTGAAAA-
1 AGAATTGAGAGTTGAAAAG
6164922 AGACATTGAGAGCATTGAAAAG
1 AGA-ATTGAGAG--TTGAAAAG
6164944 AGAATTGAGAG-TGAAAA
1 AGAATTGAGAGTTGAAAA
6164961 TGAGCACATT
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
18 9 0.26
19 7 0.21
21 15 0.44
22 3 0.09
ACGTcount: A:0.51, C:0.04, G:0.28, T:0.18
Consensus pattern (19 bp):
AGAATTGAGAGTTGAAAAG
Found at i:6166173 original size:17 final size:17
Alignment explanation
Indices: 6166151--6166203 Score: 72
Period size: 17 Copynumber: 3.1 Consensus size: 17
6166141 TGAATAATGT
6166151 TAGTTCATTAATTAAAC
1 TAGTTCATTAATTAAAC
* *
6166168 TAGTTCATTCATCAAAC
1 TAGTTCATTAATTAAAC
6166185 TAGTTCATTTAA-TAAAC
1 TAGTTCA-TTAATTAAAC
6166202 TA
1 TA
6166204 ACTCTTAATT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
17 28 0.90
18 3 0.10
ACGTcount: A:0.40, C:0.15, G:0.06, T:0.40
Consensus pattern (17 bp):
TAGTTCATTAATTAAAC
Found at i:6166633 original size:25 final size:25
Alignment explanation
Indices: 6166605--6166659 Score: 101
Period size: 25 Copynumber: 2.2 Consensus size: 25
6166595 AAGCATTCAA
6166605 GGCTGATTTAATCATCCAAACCAAG
1 GGCTGATTTAATCATCCAAACCAAG
*
6166630 GGCTGATTTAATCATTCAAACCAAG
1 GGCTGATTTAATCATCCAAACCAAG
6166655 GGCTG
1 GGCTG
6166660 TTCATATTCT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.33, C:0.22, G:0.20, T:0.25
Consensus pattern (25 bp):
GGCTGATTTAATCATCCAAACCAAG
Found at i:6171518 original size:31 final size:31
Alignment explanation
Indices: 6171475--6171550 Score: 134
Period size: 31 Copynumber: 2.5 Consensus size: 31
6171465 AAAAAAAACA
*
6171475 TAAGTTTCGGTCACCTACGATATCATTTTAT
1 TAAGTTTTGGTCACCTACGATATCATTTTAT
*
6171506 TGAGTTTTGGTCACCTACGATATCATTTTAT
1 TAAGTTTTGGTCACCTACGATATCATTTTAT
6171537 TAAGTTTTGGTCAC
1 TAAGTTTTGGTCAC
6171551 TTGGACGTTG
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.24, C:0.17, G:0.16, T:0.43
Consensus pattern (31 bp):
TAAGTTTTGGTCACCTACGATATCATTTTAT
Found at i:6174236 original size:25 final size:22
Alignment explanation
Indices: 6174207--6174269 Score: 63
Period size: 22 Copynumber: 2.7 Consensus size: 22
6174197 TTCAATAGCT
*
6174207 TATTTAATTTTTTAAAACTAAAAAA
1 TATTTAA-ATTTT-AAA-TAAAAAA
*
6174232 TATTTTAAATTTTAAATATAAAA
1 TA-TTTAAATTTTAAATAAAAAA
*
6174255 TATTTAAATATTAAA
1 TATTTAAATTTTAAA
6174270 AAATTAAATA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
22 12 0.35
23 8 0.24
24 3 0.09
25 6 0.18
26 5 0.15
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (22 bp):
TATTTAAATTTTAAATAAAAAA
Found at i:6174262 original size:15 final size:16
Alignment explanation
Indices: 6174238--6174285 Score: 66
Period size: 15 Copynumber: 3.2 Consensus size: 16
6174228 AAAATATTTT
6174238 AAAT-TTTAAATA-TA
1 AAATATTTAAATATTA
6174252 AAATATTTAAATATTA
1 AAATATTTAAATATTA
*
6174268 AAA-AATTAAATATTA
1 AAATATTTAAATATTA
6174283 AAA
1 AAA
6174286 ATACTAAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
14 4 0.13
15 22 0.71
16 5 0.16
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
AAATATTTAAATATTA
Found at i:6174278 original size:23 final size:23
Alignment explanation
Indices: 6174228--6174307 Score: 69
Period size: 23 Copynumber: 3.6 Consensus size: 23
6174218 TTAAAACTAA
* *
6174228 AAAATATTTTAAAT-TTTAAATAT
1 AAAATA-TTTAAATATTAAAAAAT
6174251 AAAATATTTAAATATTAAAAAAT
1 AAAATATTTAAATATTAAAAAAT
* * *
6174274 TAAATATTAAAAATACT-AAAAAT
1 AAAATATT-TAAATATTAAAAAAT
6174297 AAAA-A-TTAAAT
1 AAAATATTTAAAT
6174308 TACAAAAAAA
Statistics
Matches: 48, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
20 4 0.08
21 1 0.02
22 8 0.17
23 29 0.60
24 6 0.12
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.36
Consensus pattern (23 bp):
AAAATATTTAAATATTAAAAAAT
Found at i:6174282 original size:7 final size:7
Alignment explanation
Indices: 6174236--6174284 Score: 53
Period size: 7 Copynumber: 6.7 Consensus size: 7
6174226 AAAAAATATT
*
6174236 TTAAATT
1 TTAAATA
6174243 TTAAATA
1 TTAAATA
*
6174250 TAAAATA
1 TTAAATA
6174257 TTTAAATA
1 -TTAAATA
*
6174265 TTAAAAAA
1 TT-AAATA
6174273 TTAAATA
1 TTAAATA
6174280 TTAAA
1 TTAAA
6174285 AATACTAAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
7 23 0.66
8 12 0.34
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (7 bp):
TTAAATA
Found at i:6174286 original size:15 final size:15
Alignment explanation
Indices: 6174243--6174307 Score: 64
Period size: 15 Copynumber: 4.4 Consensus size: 15
6174233 ATTTTAAATT
*
6174243 TTAAATA-TAAAATAT
1 TTAAATATTAAAA-AA
6174258 TTAAATATTAAAAAA
1 TTAAATATTAAAAAA
6174273 TTAAATATTAAAAATA
1 TTAAATATTAAAAA-A
* *
6174289 CTAAA-AAT-AAAAA
1 TTAAATATTAAAAAA
6174302 TTAAAT
1 TTAAAT
6174308 TACAAAAAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
13 5 0.12
14 4 0.09
15 24 0.56
16 10 0.23
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.34
Consensus pattern (15 bp):
TTAAATATTAAAAAA
Found at i:6175037 original size:21 final size:22
Alignment explanation
Indices: 6175003--6175050 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
6174993 CGTCACATCA
* *
6175003 TCAGTCATCGTAGATTGTTATG
1 TCAGTCATCGTAGACTGTCATG
*
6175025 TCAGT-ATTGTAGACTGTCATG
1 TCAGTCATCGTAGACTGTCATG
6175046 TCAGT
1 TCAGT
6175051 GTCGTTAACT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 18 0.78
22 5 0.22
ACGTcount: A:0.23, C:0.15, G:0.23, T:0.40
Consensus pattern (22 bp):
TCAGTCATCGTAGACTGTCATG
Found at i:6191703 original size:31 final size:31
Alignment explanation
Indices: 6191640--6191714 Score: 89
Period size: 31 Copynumber: 2.4 Consensus size: 31
6191630 AATATTGCAC
*
6191640 TATTAATATAATATAACATATCATATTAAAA
1 TATTAATATAATATAACACATCATATTAAAA
* *
6191671 TATTAATATAATATATCACATCTTA-TACAAA
1 TATTAATATAATATAACACATCATATTA-AAA
* *
6191702 TAATAATAAAATA
1 TATTAATATAATA
6191715 ATCTGTCATT
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
30 2 0.05
31 36 0.95
ACGTcount: A:0.55, C:0.08, G:0.00, T:0.37
Consensus pattern (31 bp):
TATTAATATAATATAACACATCATATTAAAA
Found at i:6192626 original size:13 final size:13
Alignment explanation
Indices: 6192608--6192640 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
6192598 AAAGGAGTAA
6192608 ATGTAGAGGTTAC
1 ATGTAGAGGTTAC
6192621 ATGTAGAGGTTAC
1 ATGTAGAGGTTAC
6192634 ATGTAGA
1 ATGTAGA
6192641 AGTATATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.33, C:0.06, G:0.30, T:0.30
Consensus pattern (13 bp):
ATGTAGAGGTTAC
Found at i:6192728 original size:4 final size:4
Alignment explanation
Indices: 6192721--6192751 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
6192711 TTTATTTCAA
6192721 TATG TATG TATG TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TAT
6192752 TTTTTTACCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.26, C:0.00, G:0.23, T:0.52
Consensus pattern (4 bp):
TATG
Found at i:6201089 original size:9 final size:9
Alignment explanation
Indices: 6201035--6201424 Score: 92
Period size: 9 Copynumber: 42.6 Consensus size: 9
6201025 TGGAGAAAAT
6201035 TATAATATA
1 TATAATATA
6201044 T-T-A-ATA
1 TATAATATA
6201050 TA-AATATA
1 TATAATATA
*
6201058 TATAAAACTA
1 TATAATA-TA
6201068 TATAATA-A
1 TATAATATA
6201076 TATAATATA
1 TATAATATA
6201085 TATAA-ACTA
1 TATAATA-TA
* *
6201094 TATAAAATG
1 TATAATATA
6201103 TA-AACTATA
1 TATAA-TATA
6201112 TAT-AT-TA
1 TATAATATA
6201119 TA-AACTATA
1 TATAA-TATA
*
6201128 TAGAA-ACTA
1 TATAATA-TA
6201137 TATAATATA
1 TATAATATA
6201146 TA-AAT-TA
1 TATAATATA
* *
6201153 TGTAATTTA
1 TATAATATA
*
6201162 TAT-TTATA
1 TATAATATA
*
6201170 TATTATATA
1 TATAATATA
* *
6201179 GA-AACCATA
1 TATAA-TATA
6201188 TATGAACTATA
1 TAT-AA-TATA
*
6201199 TATACTATA
1 TATAATATA
*
6201208 TATAAAAACTA
1 TAT-AATA-TA
*
6201219 TATAGTCTATA
1 TATA--ATATA
* * *
6201230 GATAGTTTA
1 TATAATATA
6201239 TATAGACTATA
1 TATA-A-TATA
*
6201250 TAGT-TTATA
1 TA-TAATATA
6201259 TATAA-ACTA
1 TATAATA-TA
* *
6201268 TATAATTTT
1 TATAATATA
6201277 TATATATATA
1 TATA-ATATA
*
6201287 CTATGCATA-A
1 -TAT-AATATA
6201297 CTATAAATTATA
1 -TAT-AA-TATA
* *
6201309 TATATTATG
1 TATAATATA
6201318 TATAA-ACTA
1 TATAATA-TA
*
6201327 TATAATTTA
1 TATAATATA
6201336 T-TAATATA
1 TATAATATA
6201344 TAT-ATATA
1 TATAATATA
*
6201352 GT-TTATATA
1 -TATAATATA
6201361 TA-AACTATA
1 TATAA-TATA
6201370 TA-AATTATA
1 TATAA-TATA
6201379 TATAAACCATATA
1 TAT--A--ATATA
*
6201392 TATACTATA
1 TATAATATA
6201401 TATAA-ACTA
1 TATAATA-TA
6201410 TATAACTATA
1 TATAA-TATA
6201420 TATAA
1 TATAA
6201425 ACCATATATA
Statistics
Matches: 283, Mismatches: 46, Indels: 103
0.66 0.11 0.24
Matches are distributed among these distances:
6 4 0.01
7 10 0.04
8 52 0.18
9 135 0.48
10 33 0.12
11 37 0.13
12 4 0.01
13 7 0.02
14 1 0.00
ACGTcount: A:0.49, C:0.06, G:0.03, T:0.42
Consensus pattern (9 bp):
TATAATATA
Found at i:6201134 original size:27 final size:27
Alignment explanation
Indices: 6201053--6201190 Score: 82
Period size: 26 Copynumber: 5.2 Consensus size: 27
6201043 ATTAATATAA
6201053 ATATATA-TA-AAACTATATA-ATAA-T
1 ATATATATTATAAACTATATAGA-AACT
6201077 ATA-ATATATATAAACTATATAAAATGTAAACT
1 ATATATAT-TATAAACTATAT---A-G-AAACT
6201109 ATATATATTATAAACTATATAGAAACT
1 ATATATATTATAAACTATATAGAAACT
*
6201136 ATATA-ATATATAAA-T-TAT-GTAA-T
1 ATATATAT-TATAAACTATATAGAAACT
* * * *
6201159 TTATAT-TTATATATTATATAGAAACC
1 ATATATATTATAAACTATATAGAAACT
6201185 ATATAT
1 ATATAT
6201191 GAACTATATA
Statistics
Matches: 91, Mismatches: 6, Indels: 32
0.71 0.05 0.25
Matches are distributed among these distances:
22 5 0.05
23 10 0.11
24 9 0.10
25 8 0.09
26 17 0.19
27 16 0.18
28 1 0.01
29 2 0.02
31 2 0.02
32 17 0.19
33 4 0.04
ACGTcount: A:0.52, C:0.05, G:0.03, T:0.40
Consensus pattern (27 bp):
ATATATATTATAAACTATATAGAAACT
Found at i:6201158 original size:16 final size:16
Alignment explanation
Indices: 6201035--6201129 Score: 71
Period size: 16 Copynumber: 6.2 Consensus size: 16
6201025 TGGAGAAAAT
*
6201035 TATAATATATTAA-TA
1 TATAATATATAAACTA
*
6201050 TAAATATATATAAAACTA
1 TATA-ATATAT-AAACTA
6201068 TATAATA-AT--A-TA
1 TATAATATATAAACTA
6201080 -AT-ATATATAAACTA
1 TATAATATATAAACTA
* *
6201094 TATAAAATGTAAACTA
1 TATAATATATAAACTA
6201110 TAT-ATATTATAAACTA
1 TATAATA-TATAAACTA
6201126 TATA
1 TATA
6201130 GAAACTATAT
Statistics
Matches: 62, Mismatches: 7, Indels: 20
0.70 0.08 0.22
Matches are distributed among these distances:
10 3 0.05
11 4 0.06
12 2 0.03
13 2 0.03
14 2 0.03
15 7 0.11
16 32 0.52
17 5 0.08
18 5 0.08
ACGTcount: A:0.56, C:0.04, G:0.01, T:0.39
Consensus pattern (16 bp):
TATAATATATAAACTA
Found at i:6201163 original size:43 final size:43
Alignment explanation
Indices: 6201057--6201149 Score: 118
Period size: 43 Copynumber: 2.2 Consensus size: 43
6201047 ATATAAATAT
* *
6201057 ATATAAAACTATATA-ATAATATAA-TATATATAAACTATATAAA
1 ATAT-AAACTATATATATTATA-AACTATATAGAAACTATATAAA
* *
6201100 ATGTAAACTATATATATTATAAACTATATAGAAACTATATAAT
1 ATATAAACTATATATATTATAAACTATATAGAAACTATATAAA
6201143 ATATAAA
1 ATATAAA
6201150 TTATGTAATT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
42 12 0.28
43 31 0.72
ACGTcount: A:0.57, C:0.05, G:0.02, T:0.35
Consensus pattern (43 bp):
ATATAAACTATATATATTATAAACTATATAGAAACTATATAAA
Found at i:6201261 original size:20 final size:20
Alignment explanation
Indices: 6201237--6201432 Score: 145
Period size: 20 Copynumber: 9.8 Consensus size: 20
6201227 ATAGATAGTT
* *
6201237 TATATAGACTATATAGTTTA
1 TATATAAACTATATAATTTA
6201257 TATATAAACTATATAATTT-
1 TATATAAACTATATAATTTA
* **
6201276 T-TATATA-TATACT-ATGCA
1 TATATAAACTATA-TAATTTA
*
6201294 TAACTATAAATTATAT-ATATTA
1 T-A-TATAAACTATATAAT-TTA
*
6201316 TGTATAAACTATATAATTTA
1 TATATAAACTATATAATTTA
* *
6201336 TTAATATATA-TATATAGTTTA
1 -T-ATATAAACTATATAATTTA
*
6201357 TATATAAACTATATAAATTA
1 TATATAAACTATATAATTTA
* *
6201377 TATATAAACCATATATATACTA
1 TATATAAACTATATA-AT-TTA
*
6201399 TATATAAACTATATAA-CTA
1 TATATAAACTATATAATTTA
*
6201418 TATATAAACCATATA
1 TATATAAACTATATA
6201433 TACTATATAT
Statistics
Matches: 142, Mismatches: 21, Indels: 27
0.75 0.11 0.14
Matches are distributed among these distances:
17 6 0.04
18 7 0.05
19 24 0.17
20 55 0.39
21 23 0.16
22 27 0.19
ACGTcount: A:0.47, C:0.07, G:0.03, T:0.43
Consensus pattern (20 bp):
TATATAAACTATATAATTTA
Found at i:6201308 original size:26 final size:28
Alignment explanation
Indices: 6201279--6201333 Score: 78
Period size: 26 Copynumber: 2.0 Consensus size: 28
6201269 ATAATTTTTA
6201279 TATATATACTATGCAT-AACTATA-AAT
1 TATATATACTATGCATAAACTATATAAT
* *
6201305 TATATATATTATGTATAAACTATATAAT
1 TATATATACTATGCATAAACTATATAAT
6201333 T
1 T
6201334 TATTAATATA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 14 0.56
27 7 0.28
28 4 0.16
ACGTcount: A:0.45, C:0.07, G:0.04, T:0.44
Consensus pattern (28 bp):
TATATATACTATGCATAAACTATATAAT
Found at i:6201369 original size:11 final size:11
Alignment explanation
Indices: 6201355--6201442 Score: 91
Period size: 11 Copynumber: 8.6 Consensus size: 11
6201345 ATATATAGTT
6201355 TATATATAAAC
1 TATATATAAAC
*
6201366 --TATATAAAT
1 TATATATAAAC
6201375 TATATATAAAC
1 TATATATAAAC
* *
6201386 CATATATATAC
1 TATATATAAAC
6201397 TATATATAAAC
1 TATATATAAAC
6201408 --TATAT-AAC
1 TATATATAAAC
6201416 TATATATAAAC
1 TATATATAAAC
*
6201427 CATATAT--AC
1 TATATATAAAC
6201436 TATATAT
1 TATATAT
6201443 GTAAGTTATA
Statistics
Matches: 64, Mismatches: 8, Indels: 12
0.76 0.10 0.14
Matches are distributed among these distances:
8 3 0.05
9 21 0.33
10 5 0.08
11 35 0.55
ACGTcount: A:0.51, C:0.10, G:0.00, T:0.39
Consensus pattern (11 bp):
TATATATAAAC
Found at i:6201370 original size:61 final size:61
Alignment explanation
Indices: 6201237--6201466 Score: 195
Period size: 61 Copynumber: 3.8 Consensus size: 61
6201227 ATAGATAGTT
* *
6201237 TATATAGACTATATAGT-TTATATATAAACTATATAATTT-TT-ATATATATACTAT-GCATA
1 TATATAAACTATATA-TATTATATATAAACTATATAATTTATTAATATATATA-TATAGAATA
* * **
6201296 -ACTATAAATTATATATATTATGTATAAACTATATAATTTATTAATATATATATATAGTTTA
1 TA-TATAAACTATATATATTATATATAAACTATATAATTTATTAATATATATATATAGAATA
* * * * * *
6201357 TATATAAACTATATAAATTATATATAAACCATAT-ATATACTATATATAAACTATATA-ACTA
1 TATATAAACTATATATATTATATATAAACTATATAATTTATTA-ATATATA-TATATAGAATA
* * ** *
6201418 TATATAAACCATATATACTATATATGTAAGTTATATAGTTTATTAATAT
1 TATATAAACTATATATA-T-TATATATAAACTATATAATTTATTAATAT
6201467 GAACTCTCTC
Statistics
Matches: 137, Mismatches: 23, Indels: 18
0.77 0.13 0.10
Matches are distributed among these distances:
58 2 0.01
59 32 0.23
60 11 0.08
61 63 0.46
62 8 0.06
63 16 0.12
64 5 0.04
ACGTcount: A:0.46, C:0.07, G:0.03, T:0.44
Consensus pattern (61 bp):
TATATAAACTATATATATTATATATAAACTATATAATTTATTAATATATATATATAGAATA
Found at i:6201440 original size:9 final size:9
Alignment explanation
Indices: 6201340--6201442 Score: 59
Period size: 9 Copynumber: 10.8 Consensus size: 9
6201330 AATTTATTAA
6201340 TATATATA-
1 TATATATAC
*
6201348 TATAGTTTA-
1 TATA-TATAC
*
6201357 TATATAAAC
1 TATATATAC
* *
6201366 TATATAAAT
1 TATATATAC
6201375 TATATATAAACC
1 TATATAT--A-C
6201387 ATATATATAC
1 -TATATATAC
6201397 TATATATAAAC
1 TATATAT--AC
6201408 TATATA-AC
1 TATATATAC
6201416 TATATATAAAC
1 TATATAT--AC
*
6201427 CATATATAC
1 TATATATAC
6201436 TATATAT
1 TATATAT
6201443 GTAAGTTATA
Statistics
Matches: 76, Mismatches: 8, Indels: 21
0.72 0.08 0.20
Matches are distributed among these distances:
8 14 0.18
9 36 0.47
10 1 0.01
11 18 0.24
13 7 0.09
ACGTcount: A:0.50, C:0.09, G:0.01, T:0.41
Consensus pattern (9 bp):
TATATATAC
Found at i:6201454 original size:2 final size:2
Alignment explanation
Indices: 6201035--6201442 Score: 61
Period size: 2 Copynumber: 202.5 Consensus size: 2
6201025 TGGAGAAAAT
* *
6201035 TA TA -A TA TA T- TA -A TA TA AA TA TA TA TA -A AA CTA TA TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA
* * * *
6201073 TA -A TA TA -A TA TA TA TA AA CTA TA TA -A AA TG TA AA CTA TA TA
1 TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA -TA TA TA
* * * * *
6201114 TA T- TA TA AA CTA TA TA GA AA CTA TA TA -A TA TA TA AA T- TA TG
1 TA TA TA TA TA -TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA
* * * * *
6201155 TA -A TT TA TA TT TA TA TA T- TA TA TA GA AA CCA TA TA TGA -A CTA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA T-A TA -TA
* * * * *
6201197 TA TA TA CTA TA TA TA AA AA CTA TA TA GTC TA TA GA TA GTT TA TA
1 TA TA TA -TA TA TA TA TA TA -TA TA TA -TA TA TA TA TA -TA TA TA
* * * * *
6201241 TA GA CTA TA TA GTT TA TA TA TA AA CTA TA TA -A TT TT TA TA TA
1 TA TA -TA TA TA -TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA
* * * * *
6201283 TA TA CTA TG CA TA -A CTA TA AA T- TA TA TA TA T- TA TG TA TA AA
1 TA TA -TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
6201324 CTA TA TA -A TT TA T- TA -A TA TA TA TA TA TA GTT TA TA TA TA AA
1 -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA
* * * *
6201365 CTA TA TA AA T- TA TA TA TA AA CCA TA TA TA TA CTA TA TA TA AA
1 -TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA -TA TA TA TA TA
* *
6201407 CTA TA TA -A CTA TA TA TA AA CCA TA TA TA CTA TA TA T
1 -TA TA TA TA -TA TA TA TA TA -TA TA TA TA -TA TA TA T
6201443 GTAAGTTATA
Statistics
Matches: 288, Mismatches: 69, Indels: 98
0.63 0.15 0.22
Matches are distributed among these distances:
1 23 0.08
2 235 0.82
3 30 0.10
ACGTcount: A:0.49, C:0.06, G:0.03, T:0.41
Consensus pattern (2 bp):
TA
Found at i:6201454 original size:41 final size:41
Alignment explanation
Indices: 6201305--6201442 Score: 151
Period size: 41 Copynumber: 3.4 Consensus size: 41
6201295 AACTATAAAT
* * * *
6201305 TATATATATTATGTATAAACTATATAA-TTTAT-TAATA-TA
1 TATATATACTATATATAAACTATATAACTATATATAA-ACCA
* *
6201344 TATATATAGTTTATATATAAACTATATAAATTATATATAAACCA
1 TATATATA--CTATATATAAACTATAT-AACTATATATAAACCA
6201388 TATATATACTATATATAAACTATATAACTATATATAAACC-
1 TATATATACTATATATAAACTATATAACTATATATAAACCA
6201428 -ATATATACTATATAT
1 TATATATACTATATAT
6201443 GTAAGTTATA
Statistics
Matches: 88, Mismatches: 5, Indels: 12
0.84 0.05 0.11
Matches are distributed among these distances:
39 23 0.26
41 30 0.34
42 18 0.20
43 5 0.06
44 12 0.14
ACGTcount: A:0.49, C:0.07, G:0.01, T:0.43
Consensus pattern (41 bp):
TATATATACTATATATAAACTATATAACTATATATAAACCA
Found at i:6204461 original size:15 final size:15
Alignment explanation
Indices: 6204441--6204494 Score: 56
Period size: 15 Copynumber: 3.4 Consensus size: 15
6204431 AACAAAAATG
6204441 AAAAATATTTAATTA
1 AAAAATATTTAATTA
6204456 AAAAATAACTTTTAATTA
1 AAAAAT-A--TTTAATTA
*
6204474 AATGAA-ATTTAATTA
1 AA-AAATATTTAATTA
6204489 AAAAAT
1 AAAAAT
6204495 TTCATTCATA
Statistics
Matches: 32, Mismatches: 2, Indels: 10
0.73 0.05 0.23
Matches are distributed among these distances:
14 2 0.06
15 16 0.50
16 1 0.03
17 1 0.03
18 10 0.31
19 2 0.06
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (15 bp):
AAAAATATTTAATTA
Found at i:6208511 original size:13 final size:13
Alignment explanation
Indices: 6208485--6208522 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
6208475 TCACACCCCT
6208485 AATTT-TTAATATA
1 AATTTATTAA-ATA
6208498 AATTTATTAAATA
1 AATTTATTAAATA
*
6208511 AATTAATTAAAT
1 AATTTATTAAAT
6208523 TTTAATGACT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 19 0.83
14 4 0.17
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (13 bp):
AATTTATTAAATA
Found at i:6211403 original size:16 final size:16
Alignment explanation
Indices: 6211384--6211414 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
6211374 TAACTGTTCA
*
6211384 ATATTTTGATTTACTG
1 ATATATTGATTTACTG
6211400 ATATATTGATTTACT
1 ATATATTGATTTACT
6211415 ATTTATAAAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.06, G:0.10, T:0.55
Consensus pattern (16 bp):
ATATATTGATTTACTG
Found at i:6212432 original size:28 final size:28
Alignment explanation
Indices: 6212401--6212458 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
6212391 GGGGCATGAA
6212401 GATTGTATTATGTTTTATATTCGAGTCT
1 GATTGTATTATGTTTTATATTCGAGTCT
6212429 GATTGTATTATGTTTTATATTCGAGTCT
1 GATTGTATTATGTTTTATATTCGAGTCT
6212457 GA
1 GA
6212459 AACTTGATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.22, C:0.07, G:0.19, T:0.52
Consensus pattern (28 bp):
GATTGTATTATGTTTTATATTCGAGTCT
Found at i:6213639 original size:15 final size:15
Alignment explanation
Indices: 6213547--6213640 Score: 66
Period size: 15 Copynumber: 6.3 Consensus size: 15
6213537 ATAGAGTATT
*
6213547 TTCACGTAGAACATA
1 TTCACGTAGAATATA
*
6213562 TTCACTTA-ATATATA
1 TTCACGTAGA-ATATA
* *
6213577 TTCACATAG-ATATT
1 TTCACGTAGAATATA
*
6213591 TTCACGTAGAATATT
1 TTCACGTAGAATATA
* * * * *
6213606 TTTACCTATAAGATT
1 TTCACGTAGAATATA
*
6213621 TTCACGTAGAACATA
1 TTCACGTAGAATATA
6213636 TTCAC
1 TTCAC
6213641 ATATATCATA
Statistics
Matches: 62, Mismatches: 14, Indels: 6
0.76 0.17 0.07
Matches are distributed among these distances:
14 13 0.21
15 49 0.79
ACGTcount: A:0.36, C:0.17, G:0.09, T:0.38
Consensus pattern (15 bp):
TTCACGTAGAATATA
Found at i:6219131 original size:23 final size:23
Alignment explanation
Indices: 6219099--6219163 Score: 105
Period size: 23 Copynumber: 2.9 Consensus size: 23
6219089 ACTGCTCATA
6219099 TAAAT-TGCATCGAAGTGCCACG
1 TAAATATGCATCGAAGTGCCACG
6219121 TAAATATGCATCGAAGTGCCACG
1 TAAATATGCATCGAAGTGCCACG
* *
6219144 TAAATATGCACCAAAGTGCC
1 TAAATATGCATCGAAGTGCC
6219164 TCATAGATTT
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
22 5 0.12
23 35 0.88
ACGTcount: A:0.35, C:0.23, G:0.20, T:0.22
Consensus pattern (23 bp):
TAAATATGCATCGAAGTGCCACG
Found at i:6219206 original size:24 final size:25
Alignment explanation
Indices: 6219179--6219240 Score: 81
Period size: 25 Copynumber: 2.5 Consensus size: 25
6219169 GATTTCTCTT
*
6219179 GAAGGACCGCGTAG-AATTTGTCCC
1 GAAGGACCGCGTAGAAATTTATCCC
* *
6219203 GAAGGACCCCATAGAAATTTATCCC
1 GAAGGACCGCGTAGAAATTTATCCC
*
6219228 GAAGGATCGCGTA
1 GAAGGACCGCGTA
6219241 AAACCCTCGA
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
24 12 0.39
25 19 0.61
ACGTcount: A:0.31, C:0.24, G:0.26, T:0.19
Consensus pattern (25 bp):
GAAGGACCGCGTAGAAATTTATCCC
Found at i:6222554 original size:6 final size:6
Alignment explanation
Indices: 6222543--6222571 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
6222533 ACCAATTGCA
6222543 AAAAAT AAAAAT AAAAAT AAAAAT AAAAA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAA
6222572 GGTCACGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (6 bp):
AAAAAT
Found at i:6225543 original size:19 final size:17
Alignment explanation
Indices: 6225499--6225543 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
6225489 AATAAATCCC
*
6225499 TAATAAAAATGTGACAA
1 TAATAAAAATGTGAAAA
*
6225516 TAATGAAAATTGTTGAAAA
1 TAAT-AAAAATG-TGAAAA
6225535 TAATAAAAA
1 TAATAAAAA
6225544 AATGCACATG
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
17 4 0.17
18 10 0.43
19 9 0.39
ACGTcount: A:0.60, C:0.02, G:0.11, T:0.27
Consensus pattern (17 bp):
TAATAAAAATGTGAAAA
Found at i:6233539 original size:26 final size:23
Alignment explanation
Indices: 6233503--6233569 Score: 82
Period size: 26 Copynumber: 2.8 Consensus size: 23
6233493 TATTTTTTTC
6233503 AAAAGCAAAAAACAAAAAAAAGGAAA
1 AAAAGC-AAAAACAAAAAAAA--AAA
*
6233529 AAAAGGCAAAAACAAAAAAAACAA
1 AAAA-GCAAAAACAAAAAAAAAAA
6233553 AAAAGCAAAAA-AAAAAA
1 AAAAGCAAAAACAAAAAA
6233570 GCCAAAATTT
Statistics
Matches: 39, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
22 6 0.15
23 7 0.18
24 6 0.15
26 18 0.46
27 2 0.05
ACGTcount: A:0.82, C:0.09, G:0.09, T:0.00
Consensus pattern (23 bp):
AAAAGCAAAAACAAAAAAAAAAA
Found at i:6233545 original size:33 final size:33
Alignment explanation
Indices: 6233502--6233565 Score: 94
Period size: 33 Copynumber: 1.9 Consensus size: 33
6233492 CTATTTTTTT
* *
6233502 CAAAAGCAAAAAACAA-AAAAAAGGAAAAAAAGG
1 CAAAAACAAAAAA-AACAAAAAAGCAAAAAAAGG
6233535 CAAAAACAAAAAAAACAAAAAAGCAAAAAAA
1 CAAAAACAAAAAAAACAAAAAAGCAAAAAAA
6233566 AAAAGCCAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 2 0.07
33 26 0.93
ACGTcount: A:0.80, C:0.11, G:0.09, T:0.00
Consensus pattern (33 bp):
CAAAAACAAAAAAAACAAAAAAGCAAAAAAAGG
Found at i:6233546 original size:17 final size:17
Alignment explanation
Indices: 6233503--6233566 Score: 71
Period size: 17 Copynumber: 3.8 Consensus size: 17
6233493 TATTTTTTTC
6233503 AAAAGCAAAAAACAA-AA
1 AAAAGCAAAAAA-AACAA
* *
6233520 AAAAGGAAAAAAAGGC-A
1 AAAAGCAAAAAAA-ACAA
6233537 AAAA-CAAAAAAAACAA
1 AAAAGCAAAAAAAACAA
6233553 AAAAGCAAAAAAAA
1 AAAAGCAAAAAAAA
6233567 AAAGCCAAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
15 1 0.03
16 13 0.33
17 25 0.64
ACGTcount: A:0.81, C:0.09, G:0.09, T:0.00
Consensus pattern (17 bp):
AAAAGCAAAAAAAACAA
Found at i:6233562 original size:14 final size:13
Alignment explanation
Indices: 6233503--6233576 Score: 50
Period size: 13 Copynumber: 5.8 Consensus size: 13
6233493 TATTTTTTTC
6233503 AAAAGCAAAAAACA
1 AAAAGCAAAAAA-A
6233517 AAAA--AAAGGAAAA
1 AAAAGCAAA--AAAA
* *
6233530 AAAGGC-AAAAAC
1 AAAAGCAAAAAAA
*
6233542 AAAA--AAAACAA
1 AAAAGCAAAAAAA
6233553 AAAAGCAAAAAAA
1 AAAAGCAAAAAAA
*
6233566 AAAAGCCAAAA
1 AAAAGCAAAAA
6233577 TTTCAAAAAA
Statistics
Matches: 46, Mismatches: 7, Indels: 15
0.68 0.10 0.22
Matches are distributed among these distances:
11 8 0.17
12 9 0.20
13 20 0.43
14 9 0.20
ACGTcount: A:0.80, C:0.11, G:0.09, T:0.00
Consensus pattern (13 bp):
AAAAGCAAAAAAA
Found at i:6241061 original size:40 final size:41
Alignment explanation
Indices: 6241011--6241121 Score: 134
Period size: 41 Copynumber: 2.7 Consensus size: 41
6241001 GCCTTGATTT
* *
6241011 AAATGGAATTGGATTGTGAATAA-TACATGTTACTATGATC
1 AAATTGAATTGGATTGTGAATAATTACATGTTACCATGATC
* * *
6241051 TAATTGAATTGGTTTGTGAATAATTGCATGTTACCATGATC
1 AAATTGAATTGGATTGTGAATAATTACATGTTACCATGATC
* * * *
6241092 AAATTGAATTGTATTATGAATTATTTCATG
1 AAATTGAATTGGATTGTGAATAATTACATG
6241122 CTTCCCTGAT
Statistics
Matches: 59, Mismatches: 11, Indels: 1
0.83 0.15 0.01
Matches are distributed among these distances:
40 20 0.34
41 39 0.66
ACGTcount: A:0.34, C:0.07, G:0.18, T:0.41
Consensus pattern (41 bp):
AAATTGAATTGGATTGTGAATAATTACATGTTACCATGATC
Found at i:6241152 original size:82 final size:81
Alignment explanation
Indices: 6241066--6241265 Score: 222
Period size: 82 Copynumber: 2.4 Consensus size: 81
6241056 GAATTGGTTT
* ** * * * * * *
6241066 GTGAATAATTGCATGTTACCATGATCAAATTGAATTGTATTATGAATTATTTCATGCTTCC-CTG
1 GTGAATTATTGCATGTT-CCATGATTGAATTGAATCGAATTATGAATCAATGCATGCTACCAC-G
*
6241130 ATCGAATCAAGTTGAATG
64 ATCGAATCAAATTGAATG
** * *
6241148 GTGAATTATTGCATACTCATATGATTGAATTGAATCGAATTGTGAATCAATGCATGCTACCACGA
1 GTGAATTATTGCATGTTC-CATGATTGAATTGAATCGAATTATGAATCAATGCATGCTACCACGA
6241213 TCGAATCAAATTGAATG
65 TCGAATCAAATTGAATG
*
6241230 ATGAATTATTGCATGCTTCCATGATTGAATTGAATC
1 GTGAATTATTGCATG-TTCCATGATTGAATTGAATC
6241266 TAATGGTGAA
Statistics
Matches: 97, Mismatches: 18, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
81 1 0.01
82 93 0.96
83 3 0.03
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.35
Consensus pattern (81 bp):
GTGAATTATTGCATGTTCCATGATTGAATTGAATCGAATTATGAATCAATGCATGCTACCACGAT
CGAATCAAATTGAATG
Found at i:6241153 original size:41 final size:40
Alignment explanation
Indices: 6241066--6241259 Score: 140
Period size: 41 Copynumber: 4.8 Consensus size: 40
6241056 GAATTGGTTT
* * * * *
6241066 GTGAATAATTGCATG-TTACCATGATCAAATTGAATTGTATT
1 GTGAATTATTGCATGCTT-CCATGATCGAA-TCAATTGAATG
* * *
6241107 ATGAATTATTTCATGCTTCCCTGATCGAATCAAGTTGAATG
1 GTGAATTATTGCATGCTTCCATGATCGAATCAA-TTGAATG
* * * * * *
6241148 GTGAATTATTGCATAC-TCATATGATTGAATTGAATCGAATT
1 GTGAATTATTGCATGCTTC-CATGATCGAA-TCAATTGAATG
* * * *
6241189 GTGAATCAATGCATGCTACCACGATCGAATCAAATTGAATG
1 GTGAATTATTGCATGCTTCCATGATCGAATC-AATTGAATG
* *
6241230 ATGAATTATTGCATGCTTCCATGATTGAAT
1 GTGAATTATTGCATGCTTCCATGATCGAAT
6241260 TGAATCTAAT
Statistics
Matches: 114, Mismatches: 33, Indels: 12
0.72 0.21 0.08
Matches are distributed among these distances:
40 6 0.05
41 102 0.89
42 6 0.05
ACGTcount: A:0.33, C:0.14, G:0.18, T:0.36
Consensus pattern (40 bp):
GTGAATTATTGCATGCTTCCATGATCGAATCAATTGAATG
Found at i:6245865 original size:56 final size:56
Alignment explanation
Indices: 6245805--6245951 Score: 170
Period size: 60 Copynumber: 2.6 Consensus size: 56
6245795 AAATTTAATT
* *
6245805 ATTTAACTAATCATTTTCAATAAATAAATTATTTTAACTT-TGAATGATTACAATAA
1 ATTTAATTAATCATTTTCAATAAATAAATTATTTTAACTTGT-AATAATTACAATAA
* * * *
6245861 ATTTAATTAATCATGTTCACAATTCCAATAAATTATTTTAACTTGTAATAATTATAATTA
1 ATTTAATTAATCAT-TT-TCAA-T-AAATAAATTATTTTAACTTGTAATAATTACAATAA
* *
6245921 ATTTAGTTAATCATGTTCAATAAATAAATTA
1 ATTTAATTAATCATTTTCAATAAATAAATTA
6245952 CTTAATAAAA
Statistics
Matches: 76, Mismatches: 10, Indels: 10
0.79 0.10 0.10
Matches are distributed among these distances:
56 22 0.29
57 3 0.04
58 6 0.08
59 2 0.03
60 42 0.55
61 1 0.01
ACGTcount: A:0.44, C:0.09, G:0.04, T:0.44
Consensus pattern (56 bp):
ATTTAATTAATCATTTTCAATAAATAAATTATTTTAACTTGTAATAATTACAATAA
Found at i:6245900 original size:60 final size:60
Alignment explanation
Indices: 6245827--6245939 Score: 174
Period size: 60 Copynumber: 1.9 Consensus size: 60
6245817 ATTTTCAATA
*
6245827 AATAAATTATTTTAACTT-TGAATGATTACAATAAATTTAATTAATCATGTTCACAATTCC
1 AATAAATTATTTTAACTTGT-AATAATTACAATAAATTTAATTAATCATGTTCACAATTCC
* * *
6245887 AATAAATTATTTTAACTTGTAATAATTATAATTAATTTAGTTAATCATGTTCA
1 AATAAATTATTTTAACTTGTAATAATTACAATAAATTTAATTAATCATGTTCA
6245940 ATAAATAAAT
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
60 47 0.98
61 1 0.02
ACGTcount: A:0.42, C:0.09, G:0.05, T:0.44
Consensus pattern (60 bp):
AATAAATTATTTTAACTTGTAATAATTACAATAAATTTAATTAATCATGTTCACAATTCC
Found at i:6246004 original size:14 final size:13
Alignment explanation
Indices: 6245977--6246010 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
6245967 TTAATGATTT
*
6245977 TAATTAAGATTTA
1 TAATTAAGAGTTA
6245990 TAATATAAGAGTTA
1 TAAT-TAAGAGTTA
6246004 TAATTAA
1 TAATTAA
6246011 TATAATTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
13 7 0.37
14 12 0.63
ACGTcount: A:0.50, C:0.00, G:0.09, T:0.41
Consensus pattern (13 bp):
TAATTAAGAGTTA
Found at i:6246044 original size:35 final size:37
Alignment explanation
Indices: 6246005--6246081 Score: 88
Period size: 40 Copynumber: 2.1 Consensus size: 37
6245995 TAAGAGTTAT
*
6246005 AATTAAT-ATA-ATTA-ATAATTTATTATAACATTTAA
1 AATTAATCATATATTACATAATTTATTATAA-ACTTAA
*
6246040 AATTAATCATATTATTAGCATGATTTATTATAAACTTAA
1 AATTAATCATA-TATTA-CATAATTTATTATAAACTTAA
6246079 AAT
1 AAT
6246082 CTCTCAACTT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
35 7 0.20
36 3 0.09
38 4 0.11
39 8 0.23
40 13 0.37
ACGTcount: A:0.48, C:0.05, G:0.03, T:0.44
Consensus pattern (37 bp):
AATTAATCATATATTACATAATTTATTATAAACTTAA
Found at i:6246620 original size:18 final size:18
Alignment explanation
Indices: 6246588--6246622 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
6246578 TAGGTCTCGT
**
6246588 CTTGTGGACCTGGATGTG
1 CTTGTGGACAAGGATGTG
6246606 CTTGTGGACAAGGATGT
1 CTTGTGGACAAGGATGT
6246623 TTCTCAAACA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.17, C:0.14, G:0.37, T:0.31
Consensus pattern (18 bp):
CTTGTGGACAAGGATGTG
Found at i:6263566 original size:18 final size:18
Alignment explanation
Indices: 6263539--6263582 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
6263529 TATCATCTTA
* **
6263539 TTATCCTTATTATTATTC
1 TTATCATTATTAGCATTC
*
6263557 TTATCATTATTAGCATTG
1 TTATCATTATTAGCATTC
6263575 TTATCATT
1 TTATCATT
6263583 CATATCTCTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.25, C:0.14, G:0.05, T:0.57
Consensus pattern (18 bp):
TTATCATTATTAGCATTC
Found at i:6267480 original size:24 final size:26
Alignment explanation
Indices: 6267446--6267497 Score: 72
Period size: 24 Copynumber: 2.1 Consensus size: 26
6267436 ATGTAATCAT
*
6267446 ATTAAACTATAAA-ACACAT-TATAC
1 ATTAAAATATAAATACACATATATAC
*
6267470 ATTAAAATATAAATACATATATATAC
1 ATTAAAATATAAATACACATATATAC
6267496 AT
1 AT
6267498 ATCATCTTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 12 0.50
25 5 0.21
26 7 0.29
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.33
Consensus pattern (26 bp):
ATTAAAATATAAATACACATATATAC
Found at i:6269854 original size:100 final size:99
Alignment explanation
Indices: 6269669--6269855 Score: 227
Period size: 100 Copynumber: 1.9 Consensus size: 99
6269659 CAGAACAGAT
* * * *
6269669 TGCACCGAATCACTACACCTCGTGTACCACTAAGAAACTCGAGTTAGACCACGAGTGACCCATCT
1 TGCACCGAATCACTACACCTCGTGCACCACTAAGAAACTCGAGTCAGACCACGACTGACACATCT
* *
6269734 TGGTGCCATATAATGCACATATAAAGATAATCGGA
66 TGGTGCAATATAA-GAACATATAAAGATAATCGGA
* **
6269769 TGCACCGAATCACTCCACCTCGTGCACCACTAAGGTACGTCGAGTCAGACCACGACTGATACACA
1 TGCACCGAATCACTACACCTCGTGCACCACTAAGAAAC-TCGAGTCAGACCACGACTG--ACACA
6269834 -C-TGGTGCAATATCAA-AACATAT
63 TCTTGGTGCAATAT-AAGAACATAT
6269856 TCAGATTCAC
Statistics
Matches: 74, Mismatches: 9, Indels: 8
0.81 0.10 0.09
Matches are distributed among these distances:
100 40 0.54
101 27 0.36
102 3 0.04
103 4 0.05
ACGTcount: A:0.33, C:0.28, G:0.18, T:0.21
Consensus pattern (99 bp):
TGCACCGAATCACTACACCTCGTGCACCACTAAGAAACTCGAGTCAGACCACGACTGACACATCT
TGGTGCAATATAAGAACATATAAAGATAATCGGA
Found at i:6272289 original size:14 final size:14
Alignment explanation
Indices: 6272270--6272296 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
6272260 CAGGACTCGT
6272270 GGGGATTATTCAAA
1 GGGGATTATTCAAA
6272284 GGGGATTATTCAA
1 GGGGATTATTCAA
6272297 TTTTTGGGTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.33, C:0.07, G:0.30, T:0.30
Consensus pattern (14 bp):
GGGGATTATTCAAA
Found at i:6273416 original size:89 final size:89
Alignment explanation
Indices: 6273321--6273493 Score: 292
Period size: 89 Copynumber: 1.9 Consensus size: 89
6273311 ATGTTTGCGG
*
6273321 TTTACGCTAATTCTAATACTTGTAGTTTTGTTAAATTCCATTTTAGTCCTCCTTGATATGTGATT
1 TTTACGCTAATTCTAATACTTGTAGTTTTGTTAAATTCCATTTTAGTCCTCCTTGATATGCGATT
*
6273386 GTTATTTTTATTTTTCTGAAGCTC
66 GTTATTTTTAATTTTCTGAAGCTC
* * * *
6273410 TTTACGCTAATTCTAGTTCTTGTAGTTTTGTTAAATTTCATTTTAGTCCTCTTTGATATGCGATT
1 TTTACGCTAATTCTAATACTTGTAGTTTTGTTAAATTCCATTTTAGTCCTCCTTGATATGCGATT
6273475 GTTATTTTTAATTTTCTGA
66 GTTATTTTTAATTTTCTGA
6273494 TGATCTTCAT
Statistics
Matches: 78, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
89 78 1.00
ACGTcount: A:0.21, C:0.13, G:0.13, T:0.53
Consensus pattern (89 bp):
TTTACGCTAATTCTAATACTTGTAGTTTTGTTAAATTCCATTTTAGTCCTCCTTGATATGCGATT
GTTATTTTTAATTTTCTGAAGCTC
Found at i:6273988 original size:19 final size:19
Alignment explanation
Indices: 6273941--6274053 Score: 102
Period size: 19 Copynumber: 5.8 Consensus size: 19
6273931 GCATTGCGAT
6273941 TTTCTAAATTCGCAACTCGAA
1 TTTC-AAATTCGCAACT-GAA
**
6273962 AGTCAAATTCGCAACTGAA
1 TTTCAAATTCGCAACTGAA
* *
6273981 TTTCAAATTCACAACGCGAA
1 TTTCAAATTCGCAAC-TGAA
** *
6274001 AGTCAAATTCACAACTGAA
1 TTTCAAATTCGCAACTGAA
*
6274020 TTTCAAATTCGCAACGCGAA
1 TTTCAAATTCGCAAC-TGAA
*
6274040 TTT-AATTTCGCAAC
1 TTTCAAATTCGCAAC
6274054 AGGTTTTAGT
Statistics
Matches: 76, Mismatches: 14, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
19 40 0.53
20 34 0.45
21 2 0.03
ACGTcount: A:0.38, C:0.23, G:0.12, T:0.27
Consensus pattern (19 bp):
TTTCAAATTCGCAACTGAA
Found at i:6274001 original size:39 final size:39
Alignment explanation
Indices: 6273941--6274039 Score: 162
Period size: 39 Copynumber: 2.5 Consensus size: 39
6273931 GCATTGCGAT
* *
6273941 TTTCTAAATTCGCAACTCGAAAGTCAAATTCGCAACTGAA
1 TTTC-AAATTCGCAACGCGAAAGTCAAATTCACAACTGAA
*
6273981 TTTCAAATTCACAACGCGAAAGTCAAATTCACAACTGAA
1 TTTCAAATTCGCAACGCGAAAGTCAAATTCACAACTGAA
6274020 TTTCAAATTCGCAACGCGAA
1 TTTCAAATTCGCAACGCGAA
6274040 TTTAATTTCG
Statistics
Matches: 55, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
39 51 0.93
40 4 0.07
ACGTcount: A:0.39, C:0.23, G:0.12, T:0.25
Consensus pattern (39 bp):
TTTCAAATTCGCAACGCGAAAGTCAAATTCACAACTGAA
Found at i:6274042 original size:20 final size:20
Alignment explanation
Indices: 6273908--6274053 Score: 113
Period size: 20 Copynumber: 7.4 Consensus size: 20
6273898 AGTTTCCAAT
6273908 TTCGCAACGCGAATATGT-AAA
1 TTCGCAACGCGAAT-T-TCAAA
** *
6273929 -TCGCATTGCGATTTTCTAAA
1 TTCGCAACGCGAATTTC-AAA
* **
6273949 TTCGCAACTCGAAAGTCAAA
1 TTCGCAACGCGAATTTCAAA
*
6273969 TTCGCAAC-TGAATTTCAAA
1 TTCGCAACGCGAATTTCAAA
* **
6273988 TTCACAACGCGAAAGTCAAA
1 TTCGCAACGCGAATTTCAAA
* *
6274008 TTCACAAC-TGAATTTCAAA
1 TTCGCAACGCGAATTTCAAA
*
6274027 TTCGCAACGCGAATTT-AAT
1 TTCGCAACGCGAATTTCAAA
6274046 TTCGCAAC
1 TTCGCAAC
6274054 AGGTTTTAGT
Statistics
Matches: 98, Mismatches: 22, Indels: 12
0.74 0.17 0.09
Matches are distributed among these distances:
18 1 0.01
19 41 0.42
20 46 0.47
21 10 0.10
ACGTcount: A:0.36, C:0.23, G:0.14, T:0.27
Consensus pattern (20 bp):
TTCGCAACGCGAATTTCAAA
Found at i:6274814 original size:12 final size:12
Alignment explanation
Indices: 6274793--6274826 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
6274783 ACCACATTTC
*
6274793 CAATACCAAACA
1 CAATATCAAACA
6274805 CAATATCAAACA
1 CAATATCAAACA
*
6274817 CAATCTCAAA
1 CAATATCAAA
6274827 ACCCACAACC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.56, C:0.29, G:0.00, T:0.15
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:6275195 original size:9 final size:9
Alignment explanation
Indices: 6275181--6275216 Score: 54
Period size: 9 Copynumber: 4.0 Consensus size: 9
6275171 TATAACCCTG
6275181 AAGAAGAAA
1 AAGAAGAAA
*
6275190 AAGAAGAAG
1 AAGAAGAAA
6275199 AAGAAGAAA
1 AAGAAGAAA
*
6275208 AATAAGAAA
1 AAGAAGAAA
6275217 GGAAAAAGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.75, C:0.00, G:0.22, T:0.03
Consensus pattern (9 bp):
AAGAAGAAA
Found at i:6277612 original size:20 final size:20
Alignment explanation
Indices: 6277587--6277636 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
6277577 ATGTTGCGAT
6277587 CAACGCGAAAGTCAAATTCG
1 CAACGCGAAAGTCAAATTCG
*
6277607 CAACGCGAAAGTCAAATTTG
1 CAACGCGAAAGTCAAATTCG
6277627 CAACGCGAAA
1 CAACGCGAAA
6277637 CGAAATCGCA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.42, C:0.24, G:0.20, T:0.14
Consensus pattern (20 bp):
CAACGCGAAAGTCAAATTCG
Found at i:6277818 original size:25 final size:25
Alignment explanation
Indices: 6277775--6277824 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
6277765 AAATCAATTA
* *
6277775 AACATTGTTGTGGGCACATTATTTG
1 AACATTGTTATGAGCACATTATTTG
*
6277800 AACATTGTTATGAGTACATTATTTG
1 AACATTGTTATGAGCACATTATTTG
6277825 GAAAAATAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.28, C:0.10, G:0.20, T:0.42
Consensus pattern (25 bp):
AACATTGTTATGAGCACATTATTTG
Found at i:6278220 original size:18 final size:18
Alignment explanation
Indices: 6278199--6278233 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
6278189 GTAATTGGAG
6278199 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
6278217 TTTGAGTTTGAATTTCA
1 TTTGAATTTAAATTTCA
6278234 TATAAATTTC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.31, C:0.06, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:6278602 original size:39 final size:39
Alignment explanation
Indices: 6278545--6278631 Score: 147
Period size: 39 Copynumber: 2.2 Consensus size: 39
6278535 TCCGATGCTC
* *
6278545 ATCAAAATTCAAAGCTCATTTGGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
*
6278584 ATCAAAATCCAAATCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
6278623 ATCAAAATC
1 ATCAAAATC
6278632 TACAACTTGA
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 45 1.00
ACGTcount: A:0.46, C:0.20, G:0.15, T:0.20
Consensus pattern (39 bp):
ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
Found at i:6278900 original size:20 final size:20
Alignment explanation
Indices: 6278842--6278888 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
6278832 CGAAAATCGA
*
6278842 GTTGCGAATTTGACTTTCGC
1 GTTGCGAATTTGACTTTCAC
6278862 GTTGCGAATTTGACTTTCAC
1 GTTGCGAATTTGACTTTCAC
6278882 GTTGCGA
1 GTTGCGA
6278889 TTTTTACCTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.17, C:0.19, G:0.26, T:0.38
Consensus pattern (20 bp):
GTTGCGAATTTGACTTTCAC
Found at i:6280404 original size:21 final size:22
Alignment explanation
Indices: 6280378--6280432 Score: 78
Period size: 21 Copynumber: 2.6 Consensus size: 22
6280368 GTGAATCGGG
6280378 CTCTTGAACGGTGGACA-GGAC
1 CTCTTGAACGGTGGACAGGGAC
* *
6280399 CTCTTGAACGAT-GACAGGGGC
1 CTCTTGAACGGTGGACAGGGAC
6280420 CTCTTGAACGGTG
1 CTCTTGAACGGTG
6280433 AGAGGTTCTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
20 4 0.14
21 25 0.86
ACGTcount: A:0.22, C:0.24, G:0.33, T:0.22
Consensus pattern (22 bp):
CTCTTGAACGGTGGACAGGGAC
Found at i:6280469 original size:21 final size:21
Alignment explanation
Indices: 6280398--6280493 Score: 83
Period size: 21 Copynumber: 4.7 Consensus size: 21
6280388 GTGGACAGGA
* *
6280398 CCTCTTGAACGATGACAGGGG
1 CCTCTTGAATGATGAGAGGGG
* * *
6280419 CCTCTTGAACGGTGAGA-GGT
1 CCTCTTGAATGATGAGAGGGG
*
6280439 TCT-TTG-ATGATGAGAGGGG
1 CCTCTTGAATGATGAGAGGGG
**
6280458 CCTCTTGAATGAT-AGGAGGCA
1 CCTCTTGAATGATGA-GAGGGG
6280479 CCTCTTGAATGATGA
1 CCTCTTGAATGATGA
6280494 TAGGTGCATC
Statistics
Matches: 60, Mismatches: 10, Indels: 9
0.76 0.13 0.11
Matches are distributed among these distances:
18 7 0.12
19 7 0.12
20 8 0.13
21 37 0.62
22 1 0.02
ACGTcount: A:0.24, C:0.18, G:0.32, T:0.26
Consensus pattern (21 bp):
CCTCTTGAATGATGAGAGGGG
Found at i:6282774 original size:13 final size:13
Alignment explanation
Indices: 6282756--6282784 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
6282746 TTTCTTCAAT
6282756 AAAAAGACAAAAC
1 AAAAAGACAAAAC
6282769 AAAAAGACAAAAC
1 AAAAAGACAAAAC
6282782 AAA
1 AAA
6282785 GACAAATACT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.79, C:0.14, G:0.07, T:0.00
Consensus pattern (13 bp):
AAAAAGACAAAAC
Found at i:6282787 original size:11 final size:12
Alignment explanation
Indices: 6282757--6282790 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
6282747 TTCTTCAATA
6282757 AAAAGACAAAAC
1 AAAAGACAAAAC
6282769 AAAAAGACAAAAC
1 -AAAAGACAAAAC
6282782 -AAAGACAAA
1 AAAAGACAAA
6282791 TACTAACTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 9 0.43
13 12 0.57
ACGTcount: A:0.76, C:0.15, G:0.09, T:0.00
Consensus pattern (12 bp):
AAAAGACAAAAC
Found at i:6283023 original size:22 final size:22
Alignment explanation
Indices: 6282993--6283040 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
6282983 GATGGAGATA
* *
6282993 GACGGATTTCGTCGGAAATGGG
1 GACGAATTTCATCGGAAATGGG
*
6283015 GACGAATTTCATCGGAGATGGG
1 GACGAATTTCATCGGAAATGGG
6283037 GACG
1 GACG
6283041 GATGTCGCCG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.25, C:0.15, G:0.40, T:0.21
Consensus pattern (22 bp):
GACGAATTTCATCGGAAATGGG
Found at i:6283196 original size:20 final size:20
Alignment explanation
Indices: 6283171--6283335 Score: 174
Period size: 20 Copynumber: 8.2 Consensus size: 20
6283161 GCGTAAAAAC
*
6283171 ATTTGACTTTCGCATTGCGA
1 ATTTGACTTTCGCGTTGCGA
*
6283191 ATTTGAC-TTCTGTGTTGCG-
1 ATTTGACTTTC-GCGTTGCGA
* *
6283210 ATTT-ACAAATTCTCGTTGCGA
1 ATTTGAC--TTTCGCGTTGCGA
*
6283231 ATTTGACTTTTGCGTTGCGA
1 ATTTGACTTTCGCGTTGCGA
6283251 ATTTGACTTTCGCGTTGCGA
1 ATTTGACTTTCGCGTTGCGA
*
6283271 ATTTGACTTTCGCGTTGCAA
1 ATTTGACTTTCGCGTTGCGA
* *
6283291 ATTAGACTTTCGGGTTGCGA
1 ATTTGACTTTCGCGTTGCGA
* * * *
6283311 ATTTTAGTATCGTGTTGCGA
1 ATTTGACTTTCGCGTTGCGA
6283331 ATTTG
1 ATTTG
6283336 GAAAATCGCA
Statistics
Matches: 121, Mismatches: 18, Indels: 12
0.80 0.12 0.08
Matches are distributed among these distances:
18 2 0.02
19 7 0.06
20 103 0.85
21 7 0.06
22 2 0.02
ACGTcount: A:0.19, C:0.16, G:0.23, T:0.42
Consensus pattern (20 bp):
ATTTGACTTTCGCGTTGCGA
Found at i:6283352 original size:21 final size:21
Alignment explanation
Indices: 6283328--6283367 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
6283318 TATCGTGTTG
6283328 CGAATTTGGAAAATCGCAACA
1 CGAATTTGGAAAATCGCAACA
6283349 CGAATTTGGAAAATCGCAA
1 CGAATTTGGAAAATCGCAA
6283368 TGCGATTTAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.42, C:0.17, G:0.20, T:0.20
Consensus pattern (21 bp):
CGAATTTGGAAAATCGCAACA
Found at i:6288037 original size:2 final size:2
Alignment explanation
Indices: 6288030--6288055 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
6288020 ACATACATGC
6288030 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
6288056 GATAAAATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6291728 original size:22 final size:23
Alignment explanation
Indices: 6291680--6291747 Score: 84
Period size: 22 Copynumber: 3.0 Consensus size: 23
6291670 CACCACAGCT
*
6291680 CGTATAATTGCACCGAAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
* **
6291703 CGTAGAATTACACCG-AGTGCTG
1 CGTAGAATTGCACCGAAGTGCCA
*
6291725 CGTAGAATTGCACCGTAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
6291748 TATAATAATG
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
22 19 0.51
23 18 0.49
ACGTcount: A:0.28, C:0.25, G:0.25, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:6291934 original size:103 final size:103
Alignment explanation
Indices: 6291763--6291975 Score: 381
Period size: 103 Copynumber: 2.1 Consensus size: 103
6291753 TAATGTCCAT
* *
6291763 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATATGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATATGTCTCACCA
6291828 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
* * *
6291866 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAATGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATATGTCTCACCA
6291931 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
6291969 AAGGACC
1 AAGGACC
6291976 GCGTAGACCC
Statistics
Matches: 105, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
103 105 1.00
ACGTcount: A:0.37, C:0.24, G:0.13, T:0.26
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATATGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:6293372 original size:22 final size:21
Alignment explanation
Indices: 6293347--6293406 Score: 95
Period size: 20 Copynumber: 2.9 Consensus size: 21
6293337 TTCGCTTGAG
*
6293347 GGGTATCGATTCCCCATTGAAT
1 GGGTACCGATTCCCC-TTGAAT
6293369 GGGTACCGATT-CCCTTGAAT
1 GGGTACCGATTCCCCTTGAAT
6293389 GGGTACCGATTCCCCTTG
1 GGGTACCGATTCCCCTTG
6293407 CCCAGAAATC
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
20 17 0.47
21 9 0.25
22 10 0.28
ACGTcount: A:0.18, C:0.27, G:0.25, T:0.30
Consensus pattern (21 bp):
GGGTACCGATTCCCCTTGAAT
Found at i:6296406 original size:47 final size:49
Alignment explanation
Indices: 6296332--6296456 Score: 179
Period size: 46 Copynumber: 2.6 Consensus size: 49
6296322 CTGCGCTACA
*
6296332 ATTTTTTTT-TCCT-ATTTTTGGTTTTTTTTTTCTGATTTGAATGTTGAGG
1 ATTTTTTTTCTTCTGATTTTTGG--TTTTTTTTCTGATTTGAATGTTGAGG
*
6296381 A-TTTTTTTCTTCTGA-TTTTGG-TTTTTTTCTTATTTGAATGTTGAGG
1 ATTTTTTTTCTTCTGATTTTTGGTTTTTTTTCTGATTTGAATGTTGAGG
6296427 ATTTTTTTTCTTCTGATTTTTGGTTTTTTT
1 ATTTTTTTTCTTCTGATTTTTGGTTTTTTT
6296457 ATTATATGTA
Statistics
Matches: 69, Mismatches: 2, Indels: 10
0.85 0.02 0.12
Matches are distributed among these distances:
46 25 0.36
47 14 0.20
48 13 0.19
49 16 0.23
50 1 0.01
ACGTcount: A:0.11, C:0.06, G:0.15, T:0.67
Consensus pattern (49 bp):
ATTTTTTTTCTTCTGATTTTTGGTTTTTTTTCTGATTTGAATGTTGAGG
Found at i:6297383 original size:2 final size:2
Alignment explanation
Indices: 6297378--6297404 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
6297368 TTATTGATAA
6297378 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
6297405 AAAGAACAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:6299882 original size:14 final size:14
Alignment explanation
Indices: 6299863--6299918 Score: 75
Period size: 14 Copynumber: 4.3 Consensus size: 14
6299853 TGTTCGTGAA
6299863 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
6299877 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
6299891 CG-T---TTATGTT
1 CGTTCGGTTATGTT
*
6299901 CGTTCGATTATGTT
1 CGTTCGGTTATGTT
6299915 CGTT
1 CGTT
6299919 TATGTTCATT
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
10 9 0.24
11 1 0.03
13 1 0.03
14 27 0.71
ACGTcount: A:0.09, C:0.14, G:0.25, T:0.52
Consensus pattern (14 bp):
CGTTCGGTTATGTT
Found at i:6299935 original size:24 final size:23
Alignment explanation
Indices: 6299864--6299938 Score: 96
Period size: 24 Copynumber: 3.1 Consensus size: 23
6299854 GTTCGTGAAC
* *
6299864 GTTCGGTTATGTTCGTTCGGTTAT
1 GTTCGTTTATGTTCGTTC-ATTAT
6299888 GTTCGTTTATGTTCGTTCGATTAT
1 GTTCGTTTATGTTCGTTC-ATTAT
*
6299912 GTTCGTTTATGTTCATTCATTTAT
1 GTTCGTTTATGTTCGTTCA-TTAT
6299936 GTT
1 GTT
6299939 TAACCCAATC
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
23 1 0.02
24 46 0.98
ACGTcount: A:0.12, C:0.12, G:0.21, T:0.55
Consensus pattern (23 bp):
GTTCGTTTATGTTCGTTCATTAT
Found at i:6300680 original size:10 final size:10
Alignment explanation
Indices: 6300665--6300739 Score: 61
Period size: 10 Copynumber: 7.7 Consensus size: 10
6300655 GGGTCTCCAA
6300665 CGTTTATGTT
1 CGTTTATGTT
6300675 CGTTTATGTT
1 CGTTTATGTT
6300685 CGTGTTCAT-TT
1 CGT-TT-ATGTT
* **
6300696 ATGTTCGTGTT
1 -CGTTTATGTT
6300707 CGTTTATGTT
1 CGTTTATGTT
6300717 CG----TGTT
1 CGTTTATGTT
6300723 CGTTTATGTT
1 CGTTTATGTT
6300733 CGTTTAT
1 CGTTTAT
6300740 TTATTAAATG
Statistics
Matches: 51, Mismatches: 6, Indels: 16
0.70 0.08 0.22
Matches are distributed among these distances:
6 6 0.12
10 34 0.67
11 7 0.14
12 4 0.08
ACGTcount: A:0.09, C:0.12, G:0.21, T:0.57
Consensus pattern (10 bp):
CGTTTATGTT
Found at i:6300696 original size:16 final size:16
Alignment explanation
Indices: 6300671--6300735 Score: 121
Period size: 16 Copynumber: 4.1 Consensus size: 16
6300661 CCAACGTTTA
6300671 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
*
6300687 TGTTCATTTATGTTCG
1 TGTTCGTTTATGTTCG
6300703 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
6300719 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
6300735 T
1 T
6300736 TTATTTATTA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 47 1.00
ACGTcount: A:0.08, C:0.12, G:0.23, T:0.57
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:6300826 original size:16 final size:16
Alignment explanation
Indices: 6300805--6300837 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
6300795 AAAAAAATTT
6300805 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
6300821 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
6300837 T
1 T
6300838 CTATTTATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.06, C:0.12, G:0.24, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:6301780 original size:14 final size:15
Alignment explanation
Indices: 6301761--6301793 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
6301751 ATTATAATTA
6301761 TATTTTTT-TATTTT
1 TATTTTTTCTATTTT
6301775 TATTTTTTCTATTTT
1 TATTTTTTCTATTTT
6301790 TATT
1 TATT
6301794 ATAGTTTAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.15, C:0.03, G:0.00, T:0.82
Consensus pattern (15 bp):
TATTTTTTCTATTTT
Found at i:6302907 original size:59 final size:59
Alignment explanation
Indices: 6302762--6302907 Score: 156
Period size: 60 Copynumber: 2.5 Consensus size: 59
6302752 AAACATATGA
* *
6302762 ATAGTCAGGTGACCATTTTATAACTTTTAATAGTCGATGGACTCAATAAAACATCACCCT
1 ATAGTCAGGAGACCATTTTGTAACTTTTAATAGTCGA-GGACTCAATAAAACATCACCCT
** * *
6302822 ATAGTC-GGAGGGTCATTTTGTAACTTTTAATAGTC-AGAGACTCAATAAAGCAAT-ATCCT
1 ATAGTCAGGA-GACCATTTTGTAACTTTTAATAGTCGAG-GACTCAATAAAAC-ATCACCCT
*
6302881 ATAGTCAGGAGACCCTTTGTGT-ACTTT
1 ATAGTCAGGAGACCATTT-TGTAACTTT
6302908 ACCCTTACAT
Statistics
Matches: 72, Mismatches: 9, Indels: 11
0.78 0.10 0.12
Matches are distributed among these distances:
58 1 0.01
59 35 0.49
60 36 0.50
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Consensus pattern (59 bp):
ATAGTCAGGAGACCATTTTGTAACTTTTAATAGTCGAGGACTCAATAAAACATCACCCT
Found at i:6306154 original size:2 final size:2
Alignment explanation
Indices: 6306147--6306182 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
6306137 CACGATAAAC
6306147 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6306183 CAGAAAATCA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6306689 original size:78 final size:76
Alignment explanation
Indices: 6306591--6306796 Score: 268
Period size: 78 Copynumber: 2.6 Consensus size: 76
6306581 AGACCTGCAA
* *
6306591 TAAGGACTTACCCTGAGCACAAAGCAGATGAACCTATGGTAAGGACTTACCCTGAGCATAAAGCA
1 TAAGGACTTACCCTGAGCACAAAACAGA-GAACCTA-GGTAAGGACTTACCCTGAGCACAAAGCA
6306656 GAGGAGCCTACGG
64 GAGGAGCCTACGG
* * * *
6306669 TAAGGACTTACCCTGAGCACAAAACAAAGGAGCCTACAGTAAGGACTTACCCTGAGGACAAAGCA
1 TAAGGACTTACCCTGAGCACAAAACAGA-GAACCTA-GGTAAGGACTTACCCTGAGCACAAAGCA
*
6306734 GAGGAGCCTGCGG
64 GAGGAGCCTACGG
* * *
6306747 TAAGGACTTATCCTGAGCATAAAACAGAGAATCCTGAGGTAAGGTCTTAC
1 TAAGGACTTACCCTGAGCACAAAACAGAGAA-CCT-AGGTAAGGACTTAC
6306797 AAGTCATAGA
Statistics
Matches: 111, Mismatches: 15, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
77 2 0.02
78 108 0.97
79 1 0.01
ACGTcount: A:0.35, C:0.22, G:0.25, T:0.17
Consensus pattern (76 bp):
TAAGGACTTACCCTGAGCACAAAACAGAGAACCTAGGTAAGGACTTACCCTGAGCACAAAGCAGA
GGAGCCTACGG
Found at i:6306790 original size:39 final size:39
Alignment explanation
Indices: 6306591--6306775 Score: 262
Period size: 39 Copynumber: 4.7 Consensus size: 39
6306581 AGACCTGCAA
* * *
6306591 TAAGGACTTACCCTGAGCACAAAGCAGATGAACCTATGG
1 TAAGGACTTACCCTGAGCACAAAGCAGAGGAGCCTACGG
*
6306630 TAAGGACTTACCCTGAGCATAAAGCAGAGGAGCCTACGG
1 TAAGGACTTACCCTGAGCACAAAGCAGAGGAGCCTACGG
* * *
6306669 TAAGGACTTACCCTGAGCACAAAACAAAGGAGCCTACAG
1 TAAGGACTTACCCTGAGCACAAAGCAGAGGAGCCTACGG
* *
6306708 TAAGGACTTACCCTGAGGACAAAGCAGAGGAGCCTGCGG
1 TAAGGACTTACCCTGAGCACAAAGCAGAGGAGCCTACGG
* * *
6306747 TAAGGACTTATCCTGAGCATAAAACAGAG
1 TAAGGACTTACCCTGAGCACAAAGCAGAG
6306776 AATCCTGAGG
Statistics
Matches: 129, Mismatches: 17, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
39 129 1.00
ACGTcount: A:0.36, C:0.23, G:0.25, T:0.16
Consensus pattern (39 bp):
TAAGGACTTACCCTGAGCACAAAGCAGAGGAGCCTACGG
Found at i:6310418 original size:39 final size:39
Alignment explanation
Indices: 6310362--6310547 Score: 151
Period size: 39 Copynumber: 4.7 Consensus size: 39
6310352 ATGCGGTAAA
* * *
6310362 GACTTACCTTGATCACAAAGCGGAGGAGCCTACGATAAG
1 GACTTACCCTGAGCACAAAGCAGAGGAGCCTACGATAAG
* * *
6310401 GACTTACCCTGAGCACAAAGTAGAGGAGCCTACGGTACG
1 GACTTACCCTGAGCACAAAGCAGAGGAGCCTACGATAAG
* ** * * *
6310440 GACTTACCCTGAGCACAAAACATTGCAGCCTGA-GGTAAA
1 GACTTACCCTGAGCACAAAGCAGAGGAGCCT-ACGATAAG
* * * *
6310479 GACTTACCATGAGCAAAATAGAAGAGGAGCCT-CTGGTAAG
1 GACTTACCCTGAGCACAA-AGCAGAGGAGCCTAC-GATAAG
* * **
6310519 GACTTAACATGAGCACAAAATAGAGGAGC
1 GACTTACCCTGAGCACAAAGCAGAGGAGC
6310548 TTGCAGTAAG
Statistics
Matches: 118, Mismatches: 25, Indels: 8
0.78 0.17 0.05
Matches are distributed among these distances:
39 88 0.75
40 30 0.25
ACGTcount: A:0.36, C:0.22, G:0.25, T:0.17
Consensus pattern (39 bp):
GACTTACCCTGAGCACAAAGCAGAGGAGCCTACGATAAG
Found at i:6315145 original size:28 final size:29
Alignment explanation
Indices: 6315091--6315151 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 29
6315081 TTTCTTTACT
* * *
6315091 TTTC-TTCTTTTTGAGTGCTGGATTTTC-
1 TTTCTTTCTTTTGGAGTGCTGCAATTTCA
*
6315118 TTTCTTTCTTTTGGAGTGCTTCAATTTCA
1 TTTCTTTCTTTTGGAGTGCTGCAATTTCA
6315147 TTTCT
1 TTTCT
6315152 GATTTTCTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
27 4 0.14
28 19 0.68
29 5 0.18
ACGTcount: A:0.10, C:0.16, G:0.15, T:0.59
Consensus pattern (29 bp):
TTTCTTTCTTTTGGAGTGCTGCAATTTCA
Found at i:6320210 original size:39 final size:39
Alignment explanation
Indices: 6320148--6320350 Score: 219
Period size: 39 Copynumber: 5.2 Consensus size: 39
6320138 ACATATCATA
* *
6320148 AGGA-CCTATGGTAAGGGCTTACCCTGAGCACAAAGTAG
1 AGGAGCCTATGGTAAGGACTTACCCTGAGCACAAAGCAG
* * * *
6320186 AGGAGCCTGTGGTAAGGACTTACCCTGATCACAAAACAT
1 AGGAGCCTATGGTAAGGACTTACCCTGAGCACAAAGCAG
* * * * **
6320225 AAGAGCCTATGATAAGGACTTACCCTAAGCATAAAAAAG
1 AGGAGCCTATGGTAAGGACTTACCCTGAGCACAAAGCAG
* * * * *
6320264 AGGAGCATGTGGTAAGGACTTACCTTGAGTACAAAGTAG
1 AGGAGCCTATGGTAAGGACTTACCCTGAGCACAAAGCAG
* *
6320303 AGGAGCTTATGGTAAGGACTTACCCTGATCACAAAGCAG
1 AGGAGCCTATGGTAAGGACTTACCCTGAGCACAAAGCAG
*
6320342 ATGAGCCTA
1 AGGAGCCTA
6320351 CTATAAGGTC
Statistics
Matches: 132, Mismatches: 32, Indels: 1
0.80 0.19 0.01
Matches are distributed among these distances:
38 4 0.03
39 128 0.97
ACGTcount: A:0.35, C:0.19, G:0.25, T:0.20
Consensus pattern (39 bp):
AGGAGCCTATGGTAAGGACTTACCCTGAGCACAAAGCAG
Found at i:6324126 original size:39 final size:38
Alignment explanation
Indices: 6323964--6324132 Score: 153
Period size: 39 Copynumber: 4.3 Consensus size: 38
6323954 AAAGACTTGT
* * *
6323964 GGTAAGGACTTACCCTGAGCATAAAG-AAGAGATGCATGC
1 GGTAAGGACTTACCCTGAGCACAAAGAAAG-GA-GCCTAC
* * *
6324003 GGTGAGGACTTACCCTTAGCACAAGGTAAAAGG-GCCTAC
1 GGTAAGGACTTACCCTGAGCACAAAG--AAAGGAGCCTAC
* * * *
6324042 GGTAACGACTTACCCTAAGCACAAAGTAGAGGAGCCTGC
1 GGTAAGGACTTACCCTGAGCACAAAG-AAAGGAGCCTAC
*
6324081 AGTAAGGACTTACCCTGAGCACAAAGCAAAGGAGCCTAC
1 GGTAAGGACTTACCCTGAGCACAAAG-AAAGGAGCCTAC
* *
6324120 GTTAAGGTCTTAC
1 GGTAAGGACTTAC
6324133 AAGTCATAGA
Statistics
Matches: 104, Mismatches: 22, Indels: 8
0.78 0.16 0.06
Matches are distributed among these distances:
38 4 0.04
39 96 0.92
41 1 0.01
42 3 0.03
ACGTcount: A:0.34, C:0.22, G:0.26, T:0.18
Consensus pattern (38 bp):
GGTAAGGACTTACCCTGAGCACAAAGAAAGGAGCCTAC
Found at i:6324132 original size:78 final size:78
Alignment explanation
Indices: 6323964--6324132 Score: 198
Period size: 78 Copynumber: 2.2 Consensus size: 78
6323954 AAAGACTTGT
* * * * * *
6323964 GGTAAGGACTTACCCTGAGCATAAAGAAGAGATGCATGCGGTGAGGACTTACCCTTAGCACAAGG
1 GGTAAGGACTTACCCTAAGCACAAAGAAGAGATGCATGCAGTAAGGACTTACCCTGAGCACAAAG
6324029 TAAAAGGGCCTAC
66 TAAAAGGGCCTAC
* * *
6324042 GGTAACGACTTACCCTAAGCACAAAGTAGAGGA-GCCTGCAGTAAGGACTTACCCTGAGCACAAA
1 GGTAAGGACTTACCCTAAGCACAAAGAAGA-GATGCATGCAGTAAGGACTTACCCTGAGCACAAA
*
6324106 G-CAAAGGAGCCTAC
65 GTAAAAGG-GCCTAC
* *
6324120 GTTAAGGTCTTAC
1 GGTAAGGACTTAC
6324133 AAGTCATAGA
Statistics
Matches: 76, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
77 5 0.07
78 69 0.91
79 2 0.03
ACGTcount: A:0.34, C:0.22, G:0.26, T:0.18
Consensus pattern (78 bp):
GGTAAGGACTTACCCTAAGCACAAAGAAGAGATGCATGCAGTAAGGACTTACCCTGAGCACAAAG
TAAAAGGGCCTAC
Found at i:6324844 original size:25 final size:25
Alignment explanation
Indices: 6324810--6324869 Score: 111
Period size: 25 Copynumber: 2.4 Consensus size: 25
6324800 ACTAATCAAT
6324810 GGTCAACGGTTAATGGTCGAGCAAC
1 GGTCAACGGTTAATGGTCGAGCAAC
*
6324835 GGTCAACGGTTAATGGTCGAGCAAT
1 GGTCAACGGTTAATGGTCGAGCAAC
6324860 GGTCAACGGT
1 GGTCAACGGT
6324870 CGGTCAACAG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 34 1.00
ACGTcount: A:0.27, C:0.18, G:0.33, T:0.22
Consensus pattern (25 bp):
GGTCAACGGTTAATGGTCGAGCAAC
Found at i:6326844 original size:14 final size:14
Alignment explanation
Indices: 6326822--6326852 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
6326812 CATTATTTTT
6326822 TATAATTTTAAATA
1 TATAATTTTAAATA
*
6326836 TATATTTTTAAATA
1 TATAATTTTAAATA
6326850 TAT
1 TAT
6326853 TTATAATTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (14 bp):
TATAATTTTAAATA
Found at i:6335801 original size:59 final size:59
Alignment explanation
Indices: 6335738--6335853 Score: 137
Period size: 59 Copynumber: 2.0 Consensus size: 59
6335728 ACACAAATAG
* * * *
6335738 TCCATCGATTATAGGAAATTGTTTTGTTGAATCCCCT-GACTATT-AAAGTTACAAAATTC
1 TCCATCGACTATAGG-AATTGCTTTGTTGAAT-CCCTAAACTATTAAAAATTACAAAATTC
* * *
6335797 TCCATTGACTATAGGAGTTGCTTTGTTGAGTCCCTAAACTATTAAAAATTACAAAAT
1 TCCATCGACTATAGGAATTGCTTTGTTGAATCCCTAAACTATTAAAAATTACAAAAT
6335854 GGCCATTCGA
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
57 4 0.08
58 19 0.40
59 25 0.52
ACGTcount: A:0.34, C:0.16, G:0.14, T:0.36
Consensus pattern (59 bp):
TCCATCGACTATAGGAATTGCTTTGTTGAATCCCTAAACTATTAAAAATTACAAAATTC
Found at i:6338153 original size:219 final size:219
Alignment explanation
Indices: 6337548--6338523 Score: 1240
Period size: 218 Copynumber: 4.4 Consensus size: 219
6337538 GTGGACCATA
* * * * * * *
6337548 TCCTTAACACGAAGAAACCATGTTGTCACCAAATCATCTCCAAATTGACCCGATTTTCTCAACGA
1 TCCTCAACACGAAGGAACCGTGTTGTCACCAAATTATCTCTAGATTGACCCGATTTCCTCAACGA
* *
6337613 GAAGGAACAACGTCATCTTCAGCAAACAATTTACCTGAAAGCGACCAGATCTCTTCAACATGGAT
66 GAAGGAACAACGTCATCTCCAGCAAACAATTTACCTGAAAACGACCAGATCTCTTCAACATGGAT
* * *
6337678 GAGCAGTGTCGTCTTCGACACCAAAT-TTTCCAGAGTGACCCTACCTCCTCAACGCGAAGGAGCA
131 GAACAGTGTCGTCTTCAACACCAAATATTTCCAGAGTGACCCGACCTCCTCAACGCGAAGGAGCA
*
6337742 GTGTCATCCTCCTACAATCAAACT
196 GTGTCATCCTCCGACAATCAAACT
* * * * * *
6337766 ACCTTAACGCGAAAGAATCGTGTTGTCACCAAATTATCTCCAGATTGACCCGATTTCCTCAACGA
1 TCCTCAACACGAAGGAACCGTGTTGTCACCAAATTATCTCTAGATTGACCCGATTTCCTCAACGA
* * * ** * *
6337831 TAAGGAACAACGTCATCTTCAGTAAACAATTTACCTGAAAGTGACCATATCTATTTC-ACATGGA
66 GAAGGAACAACGTCATCTCCAGCAAACAATTTACCTGAAAACGACCAGATCT-CTTCAACATGGA
* * * * *
6337895 TAAACTGTGTCGTCTTCAACACCAAAAATTTCCAGAGTGACCCGACCTCCTTAACGCGAAGGAGT
130 TGAACAGTGTCGTCTTCAACACCAAATATTTCCAGAGTGACCCGACCTCCTCAACGCGAAGGAGC
*
6337960 AGTGTCATCCTCCGACAATCAGACT
195 AGTGTCATCCTCCGACAATCAAACT
* * *
6337985 TCCTCAACGCGAAGGAACCGTGTTGTCA-CAAATTATCTCTAGATTGACCTGATTTCCACAACGA
1 TCCTCAACACGAAGGAACCGTGTTGTCACCAAATTATCTCTAGATTGACCCGATTTCCTCAACGA
** *
6338049 GAAGGAACAGTGTCATCTCCAGCAAACAATTTACCTGAAAACGACCAGATCTCTTCAACATGGGT
66 GAAGGAACAACGTCATCTCCAGCAAACAATTTACCTGAAAACGACCAGATCTCTTCAACATGGAT
* * * * *
6338114 GAGCAGTGTCGTCTTCAACTCCAAATTATTTCTAGAGTGACCCGACCTCCTCAACGTGAAAGAGC
131 GAACAGTGTCGTCTTCAACACCAAA-TATTTCCAGAGTGACCCGACCTCCTCAACGCGAAGGAGC
* *
6338179 AGTGTCATCCTTCGATAATCAAACT
195 AGTGTCATCCTCCGACAATCAAACT
* * * *
6338204 TCCTCAACACGAAGGAACTGTGTTGTCACCAAAATTATCTCTTGATTGTCCCAATTTCCTCAACG
1 TCCTCAACACGAAGGAACCGTGTTGTCACC-AAATTATCTCTAGATTGACCCGATTTCCTCAACG
* *
6338269 AGAAGGAACAACGTCATCTCCAGCAAACAATTTACCTGAAAAACGACAAGATCTCTTCAACAAGG
65 AGAAGGAACAACGTCATCTCCAGCAAACAATTTACCTG-AAAACGACCAGATCTCTTCAACATGG
* * * * *
6338334 ATGAACAGTGTCGTCTTCAACTCCAAAGTATTTCCATATTGACCCGATCTCCTCAACGCAAAGGA
129 ATGAACAGTGTCGTCTTCAACACCAAA-TATTTCCAGAGTGACCCGACCTCCTCAACGCGAAGGA
* * * * *
6338399 GCAATTTCATCCTCAGACAATCAGATT
193 GCAGTGTCATCCTCCGACAATCAAACT
* * *
6338426 TCCTCAACACGAAGGAACTGTGTTGTCTCCAAATTATCTCTAGATTGACCCGATTTTCTCAAAC-
1 TCCTCAACACGAAGGAACCGTGTTGTCACCAAATTATCTCTAGATTGACCCGATTTCCTC-AACG
** * ** *
6338490 AGAAGGTGCAATGTCATCTTTAACAAACAATTTA
65 AGAAGGAACAACGTCATCTCCAGCAAACAATTTA
6338524 TCTCAAAATA
Statistics
Matches: 657, Mismatches: 93, Indels: 13
0.86 0.12 0.02
Matches are distributed among these distances:
217 3 0.00
218 238 0.36
219 165 0.25
220 1 0.00
221 119 0.18
222 131 0.20
ACGTcount: A:0.32, C:0.26, G:0.16, T:0.25
Consensus pattern (219 bp):
TCCTCAACACGAAGGAACCGTGTTGTCACCAAATTATCTCTAGATTGACCCGATTTCCTCAACGA
GAAGGAACAACGTCATCTCCAGCAAACAATTTACCTGAAAACGACCAGATCTCTTCAACATGGAT
GAACAGTGTCGTCTTCAACACCAAATATTTCCAGAGTGACCCGACCTCCTCAACGCGAAGGAGCA
GTGTCATCCTCCGACAATCAAACT
Found at i:6341613 original size:35 final size:34
Alignment explanation
Indices: 6341520--6341620 Score: 96
Period size: 35 Copynumber: 2.9 Consensus size: 34
6341510 ACTCAAGATT
* * *
6341520 TTATCTCACTTGAGAATT-TTCTTCTCAAAATAAAT
1 TTATCTCACTTGAG-ATTCTT-TTCTTAAAAAAAAA
* * *
6341555 TTCGTCTCTCTTGATATTGCTTTTCTTAAAAAAAAA
1 TT-ATCTCACTTGAGATT-CTTTTCTTAAAAAAAAA
6341591 TTATCTCACTTGAGATTACTTTTCTTAAAA
1 TTATCTCACTTGAGATT-CTTTTCTTAAAA
6341621 TAGATTTCAT
Statistics
Matches: 53, Mismatches: 10, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
35 29 0.55
36 22 0.42
37 2 0.04
ACGTcount: A:0.32, C:0.17, G:0.07, T:0.45
Consensus pattern (34 bp):
TTATCTCACTTGAGATTCTTTTCTTAAAAAAAAA
Found at i:6343270 original size:5 final size:5
Alignment explanation
Indices: 6343260--6343340 Score: 62
Period size: 5 Copynumber: 16.0 Consensus size: 5
6343250 ATAAATATAA
* *
6343260 AAAAT AAAAT AAAAT AGACAT AAAGAT AAAAT AAAGCA- AAAAG AAAAT
1 AAAAT AAAAT AAAAT A-AAAT AAA-AT AAAAT AAA--AT AAAAT AAAAT
*
6343308 -AAAT -AAAT -AAAT AAAAT AAAACA AAAAT AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAA-T AAAAT AAAAT
6343341 TGAAGAAGAA
Statistics
Matches: 64, Mismatches: 5, Indels: 14
0.77 0.06 0.17
Matches are distributed among these distances:
4 13 0.20
5 34 0.53
6 16 0.25
7 1 0.02
ACGTcount: A:0.75, C:0.04, G:0.05, T:0.16
Consensus pattern (5 bp):
AAAAT
Found at i:6343317 original size:8 final size:9
Alignment explanation
Indices: 6343249--6343340 Score: 52
Period size: 8 Copynumber: 10.3 Consensus size: 9
6343239 AAAGAATATC
6343249 AATAAATATA
1 AATAAATA-A
6343259 AA-AAATAA
1 AATAAATAA
6343267 AATAAAATAGA
1 AAT-AAATA-A
*
6343278 CATAAAGATAA
1 AAT-AA-ATAA
**
6343289 AATAAA-GC
1 AATAAATAA
*
6343297 AA-AAAGAA
1 AATAAATAA
6343305 AATAAAT-A
1 AATAAATAA
6343313 AATAAATAA
1 AATAAATAA
*
6343322 AATAAA-AC
1 AATAAATAA
6343330 AA-AAATAA
1 AATAAATAA
6343338 AAT
1 AAT
6343341 TGAAGAAGAA
Statistics
Matches: 64, Mismatches: 9, Indels: 19
0.70 0.10 0.21
Matches are distributed among these distances:
7 6 0.09
8 21 0.33
9 16 0.25
10 9 0.14
11 9 0.14
12 3 0.05
ACGTcount: A:0.75, C:0.03, G:0.04, T:0.17
Consensus pattern (9 bp):
AATAAATAA
Found at i:6343535 original size:43 final size:44
Alignment explanation
Indices: 6343474--6343557 Score: 161
Period size: 43 Copynumber: 1.9 Consensus size: 44
6343464 AATAACAATG
6343474 AAATAAAAATAATTAAATAAAACAGAACAAAAAAAGTAAAAAAA
1 AAATAAAAATAATTAAATAAAACAGAACAAAAAAAGTAAAAAAA
6343518 AAATAAAAA-AATTAAATAAAACAGAACAAAAAAAGTAAAA
1 AAATAAAAATAATTAAATAAAACAGAACAAAAAAAGTAAAA
6343558 TACCCACTGT
Statistics
Matches: 40, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
43 31 0.77
44 9 0.22
ACGTcount: A:0.77, C:0.05, G:0.05, T:0.13
Consensus pattern (44 bp):
AAATAAAAATAATTAAATAAAACAGAACAAAAAAAGTAAAAAAA
Found at i:6343556 original size:19 final size:19
Alignment explanation
Indices: 6343491--6343557 Score: 53
Period size: 21 Copynumber: 3.3 Consensus size: 19
6343481 AATAATTAAA
6343491 TAAAACAGAACAAAAAAAG
1 TAAAACAGAACAAAAAAAG
* * * *
6343510 TAAAAAAAAAATAAAAAAATTAAA
1 T--AAAACAGA-ACAAAAA--AAG
6343534 TAAAACAGAACAAAAAAAG
1 TAAAACAGAACAAAAAAAG
6343553 TAAAA
1 TAAAA
6343558 TACCCACTGT
Statistics
Matches: 35, Mismatches: 8, Indels: 10
0.66 0.15 0.19
Matches are distributed among these distances:
19 8 0.23
21 12 0.34
22 12 0.34
24 3 0.09
ACGTcount: A:0.78, C:0.06, G:0.06, T:0.10
Consensus pattern (19 bp):
TAAAACAGAACAAAAAAAG
Done.